EP3623478A1 - Vecteur rétroviral avec cassette de mini-promoteur - Google Patents

Vecteur rétroviral avec cassette de mini-promoteur Download PDF

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EP3623478A1
EP3623478A1 EP19190376.4A EP19190376A EP3623478A1 EP 3623478 A1 EP3623478 A1 EP 3623478A1 EP 19190376 A EP19190376 A EP 19190376A EP 3623478 A1 EP3623478 A1 EP 3623478A1
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Prior art keywords
promoter
pac3
cells
retrovirus
vector
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Harry E. Gruber
Douglas J. Jolly
Amy H. Lin
Christopher R. Logg
Noriyuki Kasahara
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Tocagen Inc
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Tocagen Inc
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    • C12Y305/04001—Cytosine deaminase (3.5.4.1)

Definitions

  • This disclosure relates to retroviral replicating vectors (RRV) for treating cell proliferative.
  • the disclosure further relates to the use of such retroviral replicating vectors for delivery and expression of heterologous nucleic acids.
  • Replicating retroviral vectors have been used to selectively infect tumors in animal models ( Wang et al., Hum. Gene. Ther., 14:117-127, 2003 , Tai et al., Mol Ther, 12:842-851, 2005 ), where replication occurs through the tumor.
  • the conventional strategy for transgene expression has been to use an IRES component to allow internal initiation of translation from the internal ribosome binding site.
  • the IRES component is about 600bp leaving approximately 900 bp for coding sequence in size-limited vectors.
  • the tumor can be eliminated or growth/spreading inhibited by subsequent treatment with prodrugs (e.g., 5-fluorocytosine, which is converted in situ by cytosine deaminase to the anti-cancer drug 5-fluorouracil ( Tai et al., Mol Ther., 12:117-127, 2005 , Ostertag et al., Neuro Oncol., 2012 )).
  • prodrugs e.g., 5-fluorocytosine, which is converted in situ by cytosine deaminase to the anti-cancer drug 5-fluorouracil ( Tai et al., Mol Ther., 12:117-127, 2005 , Ostertag et al., Neuro Oncol., 2012 )
  • prodrugs e.g., 5-fluorocytosine, which is converted in situ by cytosine deaminase to the anti-cancer drug 5-fluorouracil ( Tai et al., Mol Ther., 12:117-
  • RRVtk herpes thymidine kinase
  • ganciclovir acyclovir
  • valacyclovir valacyclovir
  • the HSVtk gene has a coding sequence of just over 1.1kb and when combined with with an IRES used in some expression constructs results in an insert of greater than about 1.6kb. This size is not sufficiently stable for clinical use.
  • Another example is the combination of the cytosine deamine gene (SEQ ID NO:1 or 3) with the UPRT gene (SEQ ID NO:7) or OPRT gene ( WO2010036986 , Perez et al., Mol. Ther., 2005 ), where these fusion genes are about 1200bp. When combined with an IRES the size exceeds about 1.8kb and showed undesirable instability although expression, before deletions occurred, was satisfactory.
  • This disclosure provides methods and compositions that allow the stable expression in vivo of a gene or multiple genes exceeding a total size of about 0.9 kb in a replicating vector.
  • the disclosure provides vectors comprising at least one mini-promoter cassette capable of expressing heterologous gene(s) that can be greater than 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, or 1.9 kb. If one considers a therapeutic cassette to be a plurality of mini-promoter cassettes or a single mini-promoter cassette and a second cassette comprising a polIII promoter or IRES operably linked to a second therapeutic molecule then the overall therapeutic cassette can comprise about 1.2-2.0 kb. For example, where two mini-promoter cassettes are present in a therapeutic cassette, a first mini-cassette can express a first gene or therapeutic molecule, while the second cassette can express a second gene or therapeutic molecule.
  • a recombinant replication competent retrovirus comprising: a retroviral GAG protein; a retroviral POL protein; a retroviral envelope (ENV); a retroviral polynucleotide comprising Long-Terminal Repeat (LTR) sequences at the 3' end of the retroviral polynucleotide sequence, a promoter sequence at the 5' end of the retroviral polynucleotide, said promoter being suitable for expression in a mammalian cell, a gag nucleic acid domain, a pol nucleic acid domain and an env nucleic acid domain; a therapeutic cassette comprising at least one mini-promoter operably linked to a heterologous polynucleotide, wherein the cassette is positioned 5' to the
  • the therapeutic cassette comprises a least one core- or mini-promoter and enhancer operably linked to a heterologous polynucleotide.
  • the retroviral polynucleotide sequence is derived from a gamma retrovirus, such as murine leukemia virus (MLV), Moloney murine leukemia virus (MoMLV), Feline leukemia virus (FeLV), Baboon endogenous retrovirus (BEV), porcine endogenous virus (PERV), the cat derived retrovirus RD114, squirrel monkey retrovirus, Xenotropic murine leukemia virus-related virus (XMRV), avian reticuloendotheliosis virus (REV), or Gibbon ape leukemia virus (GALV).
  • MMV murine leukemia virus
  • MoMLV Moloney murine leukemia virus
  • FeLV Feline leukemia virus
  • BEV Baboon endogenous retrovirus
  • PERV porcine endogenous virus
  • the MLV is an amphotropic MLV or an ecotropic MLV with an amphotropic or GALV envelope gene.
  • the retrovirus is an oncoretrovirus or gamma retrovirus.
  • the vector comprises the mini-promoter cassette can infect a mammalian target cell.
  • the target cell is a cell having having aberrant proliferative capactity such as those associated with a cell proliferative disorder.
  • the cell proliferative disorder can be selected from the group consisting of, but is not limited to, neoplasias and autoimmune diseases.
  • the promoter for transcription of the RRV genome comprises a CMV promoter.
  • the promoter comprises a CMV-R-U5 domain polynucleotide.
  • the CMV-R-U5 domain comprises the immediately early promoter from human cytomegalovirus linked to an MLV R-U5 region.
  • the gag and pol of the polynucleotide are derived from an oncoretrovirus or gamma retrovirus.
  • the env domain encodes an amphotropic ENV protein.
  • the therapeutic cassette comprises at least one mini-promoter cassette and can also include an enhancer and which comprises a therapeutic (heterologous) polynucleotide sequence that upon expression codes for a therapeutic protein or a therapeutic nucleic acid (e.g., an siRNA, shRNA, microRNA or the like).
  • the mini-promoter cassette is a promoter for RNA polymerase II.
  • the mini-promoter cassette is a promoter for RNA polymerase III (e.g., a U6 promoter).
  • the therapeutic cassette comprises a single mini-promoter cassette comprising a mini-promoter and enhancer operably linked to a coding sequence for a therapeutic molecule or molecules.
  • the therapeutic cassette comprises at least one mini-promoter cassette and a second cassette.
  • the second cassette may be a second mini-promoter cassette, an IRES cassette or a polIII promoter cassette.
  • the mini-promoter promotes transcription of an operably linked gene or coding nucleic acid sequence.
  • a mini-promoter includes the minimal amount of elements necessary for effective transcription and/or translation of an operably linked coding sequence and has better expression than a core promoter.
  • a mini-promoter can include a core promoter, but also includes additional regulatory domains that promote transcription.
  • a mini-promoter is about 100-600 bp in length while a core promoter is typically less than about 100bp ( e.g., about 70-80 bp).
  • a second cassette e.g., a second mini-promoter cassette, polIII promoter cassette or IRES cassette
  • the cassette will typically comprise an enhancer element or another element either upstream or downstream of the core promoter sequence that facilitates expression of an operably linked coding sequence above the expression levels of the core promoter alone.
  • the disclosure provides small regulatory promoter domains (e.g., modified core promoters) derived from either cellular elements as determined for "core promoter" elements ( ⁇ 100, ⁇ 200, ⁇ 400 or ⁇ 600 bp) that allow ubiquitous expression at significant levels in target cells and are useful for stable incorporation into vectors, in general, and replicating retroviral vectors, in particular, to allow efficient expression of transgenes.
  • core promoters plus minimal enhancer sequences to allow better gene expression that are still under 200, 400 or 600bp.
  • Such enhanced promoters include modified core promoters, naturally occurring tissue specific promoters, small viral promoters such as the Rous Sarcoma virus derived promoters.
  • the therapeutic cassette comprising at least one mini-promoter cassette will have expression levels that are greater than or about equal to or about 1 fold to 2 fold less than the expression levels of an IRES cassette with the same gene.
  • the vector can comprise any number of different heterologous polynucleotides operably Inked to a core- or mini-promoter.
  • the heterologous polynucleotide can comprise a cytokine gene, an siRNA, microRNA or RNAi molecules, a targeting sequence, a binding domain, a cytotoxic gene, a single chain antibody or any combination thereof.
  • the heterologous polynucleotide is a non-translated RNA such as siRNA, microRNA or RNAi then no mini-promoter may be necessary, but may be included in combination with a transcribed gene.
  • the heterologous polynucleotide comprises a polynucleotide having a sequence as set forth in SEQ ID NO: 3 (CDopt-3pt), 5 (CDopt), 11 (CDopt-UPRT), 13 (CDopt-linker-UPRT), 15 (CDopt3-OPRT), 17 (CDopt3-linker-OPRT), or 75 (HSVtkopt).
  • the heterologous sequence encodes a polypeptide comprising a sequence as set forth in SEQ ID NO: 4 or 76.
  • the heterologous nucleic acid is human codon optimized and encodes a polypeptide as set forth in SEQ ID NO:4 or 76.
  • the disclosure provides an isolated polynucleotide comprising from 5' to 3': a CMV-R-U5 fusion of the immediate early promoter from human cytomegalovirus to an MLV R-U5 region; a PBS, primer binding site for reverse transcriptase; a 5' splice site; ⁇ packaging signal; a gag coding sequence for MLV group specific antigen; a pol coding sequence for MLV polymerase polyprotein; a 3' splice site; a 4070A env coding sequence for envelope protein of MLV strain 4070A; at least one mini-promoter cassettes operably linked to a therapeutic gene; a polypurine tract; and a U3-R-U5 MLV long terminal repeat.
  • the 3' LTR is derived from an oncoretrovirus or gamma-retrovirus.
  • the 3' LTR comprises a U3-R-U5 domain.
  • the disclosure provides a method of treating a cell proliferative disorder in a subject comprising contacting the subject or cell with a retrovirus of the disclosure, wherein the heterologous nucleic acid sequence encodes a therapeutic protein that inhibits proliferation of a neoplastic cell.
  • the retrovirus comprises a polynucleotide encoding a polypeptide having a sequence as set forth in SEQ ID NO: 4, 12, 14, 16, 18 or 76, wherein the polynucleotide is operably linked to a mini-promoter.
  • SEQ ID NO:19 depicts a pAC3-C1.yCD2 vector wherein the vector comprises a gag, pol and env sequence, the env sequence immediately followed by a promoter CMV core promoter and a humanized cytosine deaminase with 3 heat stabilized mutation, which is then followed by the 3' LTR.
  • SEQ ID NO:20 depicts a similar structure however, the cassette comprises an S1 promoter followed by the transgene of human GMCSF.
  • SEQ ID NO:21 shows the sequence of a an RRV vector "pACE-CD".
  • SEQ ID NO:22 shows a sequence similar to SEQ ID NO:19 and 20 except the promoter cassette comprises an S1 promoter operably linked to murine GMCSF.
  • SEQ ID NO:39 shows the sequence of an RRV having an S1-yCD2 cassette.
  • SEQ ID NO:40 shows the sequence of an RRV having a C1-GFP cassette.
  • SEQ ID NO:41 shows the sequence of an RRV having an S1-GFP cassette.
  • Other vectors of the disclosure comprising mini-promoters linked to heterologous nucleic acids are set forth in SEQ ID NOs:77-85 and 86.
  • the disclosure provides a vector comprising a recombinant replication competent retrovirus (RRV) and having a mini-promoter cassette, wherein the vector infects a target cell multiple times leading to a mean of 3 or more copies of the retrovirus genome per target cell.
  • the multiple copies provide a "super" infection useful for gene delivery and protein production in vivo and in vitro.
  • the RRV comprises: a retroviral GAG protein; a retroviral POL protein; a retroviral envelope; a retroviral polynucleotide comprising Long-Terminal Repeat (LTR) sequences at the 3' end of the retroviral polynucleotide sequence, a promoter sequence at the 5' end of the retroviral polynucleotide, said promoter being suitable for expression in a mammalian cell, a gag nucleic acid domain, a pol nucleic acid domain and an env nucleic acid domain; a cassette comprising at least one mini-promoter or core-promoter and enhancer operably linked to a heterologous polynucleotide, wherein the cassette is positioned 5' to the 3' LTR and 3' to the env nucleic acid domain encoding the retroviral envelope; and cis-acting sequences necessary for reverse transcription, packaging and integration in a target cell, wherein the RRV maintains higher
  • the retroviral polynucleotide sequence is derived from murine leukemia virus (MLV), Moloney murine leukemia virus (MoMLV),Feline leukemia virus (FeLV), Baboon endogenous retrovirus (BEV), porcine endogenous virus (PERV), the cat derived retrovirus RD114, squirrel monkey retrovirus, Xenotropic murine leukemia virus-related virus (XMRV), avian reticuloendotheliosis virus (REV), or Gibbon ape leukemia virus (GALV).
  • the MLV is an amphotropic MLV.
  • the retrovirus is an oncoretrovirus or gamma retrovirus.
  • the target cell is a cell having aberrant cell proliferative capacity such as those associated with a cell proliferative disorder (e.g., a cancer cell).
  • the cell proliferative disorder can be selected from the group consisting of, but is not limited to, lung cancer, colon-rectum cancer, breast cancer, prostate cancer, urinary tract cancer, uterine cancer, brain cancer, head and neck cancer, pancreatic cancer, melanoma, stomach cancer and ovarian cancer, lymphoma, leukemia, rheumatoid arthritis and other autoimmune diseases.
  • the vector can comprise a promoter to drive transcription of the gag, pol and env such as a CMV promoter having a sequence as set forth in SEQ ID NO:19, 20 or 22 from nucleotide 1 to about nucleotide 582 and may include modification to one or more nucleic acid bases and which is capable of directing and initiating transcription.
  • the promoter comprises a sequence as set forth in SEQ ID NO: 19, 20 or 22 from nucleotide 1 to about nucleotide 582.
  • the promoter comprises a CMV-R-U5 domain polynucleotide.
  • the CMV-R-U5 domain comprises the immediately early promoter from human cytomegalovirus linked to an MLV R-U5 region.
  • the CMV-R-U5 domain polynucleotide comprises a sequence as set forth in SEQ ID NO: 19, 20 or 22 from about nucleotide 1 to about nucleotide 1202 or sequences that are at least 95% identical to a sequence as set forth in SEQ ID NO: 19, 20 or 22, wherein the polynucleotide promotes transcription of a nucleic acid molecule operably linked thereto.
  • the gag and pol of the polynucleotide are derived from an oncoretrovirus or gamma retrovirus.
  • the gag nucleic acid domain can comprise a sequence from about nucleotide number 1203 to about nucleotide 2819 of SEQ ID NO: 19 or 22 or a sequence having at least 95%, 98%, 99% or 99.8% identity thereto.
  • the pol domain can comprise a sequence from about nucleotide number 2820 to about nucleotide 6358 of SEQ ID NO: 19 or 22 or a sequence having at least 95%, 98%, 99% or 99.9% identity thereto.
  • the env domain encodes an amphotropic env protein.
  • the env domain can comprise a sequence from about nucleotide number 6359 to about nucleotide 8323 of SEQ ID NO: 19 or 22 or a sequence having at least 95%, 98%, 99% or 99.8% identity thereto.
  • the mini-promoter of the vector can be any regulatory domain that is smaller than 600 bp ( e.g., about 600 bp, 550 bp, 500 bp, 450 bp, 400 bp, 350 bp, 300 bp, 250 bp, 200 bp, 150 bp, 100 bp, about 90 bp, about 80 bp, about 76 bp, about 74 bp or smaller) and allows for transcription of an operably linked coding sequence or non-coding sequence.
  • 600 bp e.g., about 600 bp, 550 bp, 500 bp, 450 bp, 400 bp, 350 bp, 300 bp, 250 bp, 200
  • the mini-promoter comprises a sequence from about nucleotide number 8330 to about nucleotide 8406 of SEQ ID NO: 19 or 22 or a sequence having at least 95%, 98%, or 99% identity thereto.
  • the mini-promoter comprises a sequence selected from the group consisting of SEQ ID NO:56, 57, 59, 65, 67, 68, 69, 71, 72, 73, and 74.
  • the disclosure provides methods and compositions useful for gene or protein delivery to a cell or subject. Such methods and compositions can be used to treat various diseases and disorders in a subject including cancer and other cell proliferative diseases and disorders.
  • the disclosure provides retroviral replicating vectors for gene delivery utilizing core-promoter and/or mini-promoter cassettes operably linked to a heterologous polynucleotide to be expressed.
  • a size of about 1.5kb stability of transgenes in RRV vectors can be variable.
  • the conventional strategy for transgene expression following the successful cloning of an IRES cassette into MLV has been to use an IRES component to allow internal initiation of translation from the internal ribosome binding site.
  • the IRES component is about 600bp leaving approximately 900 bp for coding sequence. Accordingly, the size of the polynucleotide linked to the IRES cassette is limited by stability.
  • One alternative to increase the size of the polynucleotide to be expressed or delivered is to use a smaller regulatory sequence that promotes transcription such as a promoter, promoter/enhancer, or other regulatory domains.
  • promoters are rather large; typically over 600bp for full functionality and the full size of a promoter can be many kilobases. Smaller promoters can be generated that allow reliable expression of transgenes in mammalian cells from vectors such as replicating retroviral vectors (RRVs).
  • RRVs retroviral vectors
  • one possible solution is to use the "core" promoters described by Kadanaga and collaborators ( Juven-Gershon et al., Nature Methods, 11:917-922, 2006 ). These core promoters are based on the adenovirus major late (AdML) and cytomegalovirus (CMV) major immediate early genes, and the synthetic "super core promoter" SCP1.
  • cellular core promoters include, but are not limited to, the human heme oxygenase proximal promoter (121 bp; Tyrrell et al., Carcinogenesis, 14: 761-765, 1993 ), the CTP:phosphocholine cytidylyltransferase (CCT) promoter (240bp; Zhou et al., Am. J. Respir. Cell Mol. Biol., 30: 61-68, 2004 ); the Human ASK (for Activator of S phase Kinase, also known as HsDbf4 gene, 63bp; Yamada et al.
  • these "core" promoters can be used as a starting point for further modifications to improve the activity of the promoter. For example, such modifications including the additional of other domains and sequences to the "core" promoter to improve functionality (e.g., enhancers, Kozak sequences and the like). In one embodiment, such further modifications can includes the addition of enhancers.
  • the length of these core promoters are approximately 70-80 bp each, thus leaving approximately 1.4 kb of capacity for transgene sequence.
  • the use of such promoters can give useful expression of genes such as the HSVtk gene which is >1.1kb long.
  • such promoters are not always reliable for obtaining levels of expression equivalent to or better than those from the IRES driven expression vectors.
  • the two CMV and Adenovirus derived core-promoters are even less reliable than the synthetic SCP1 promoter.
  • core promoters Juven-Gershon et al., Nat. Methods, 2006 ; Juven-Gershon and Kadonaga Dev. Biol. 339:225-229, 2010 ), as described herein, although not as effective as an IRES, allow expression of longer genes, which have therapeutic benefit.
  • various promoter-components can be used to optimize expression and stability of the RRV.
  • Such optimized core promoters provide a more effective expression and stability of the viral polynucleotide.
  • "designer" promoters can comprise a core promoter that has been further modified to include one or more additional elements suitable for stability and expression.
  • the use of such core promoters either alone or including additional elements for expression can be used in various vectors including replication competent retroviral vectors.
  • the disclosure provides a RRV comprising a therapeutic cassette 3' to the env coding sequence and 5' to the 3' LTR.
  • therapeutic cassette a domain within the RRV that comprises at least one mini-promoter cassette or a core-promoter cassette and one additional cassette (e.g., an IRES, polIII or minipromoter cassette), wherein a therapeutic polynucleotide sequence that upon expression codes for a therapeutic protein (e.g ., cytosine deaminse, thymidine kinase and the like) or a therapeutic nucleic acid (e.g ., an siRNA, shRNA, microRNA or the like).
  • a therapeutic protein e.g cytosine deaminse, thymidine kinase and the like
  • a therapeutic nucleic acid e.g ., an siRNA, shRNA, microRNA or the like.
  • a "therapeutic cassette” can comprise a single mini-promoter cassette comprising a mini-promoter operably linked to a coding sequence for a therapeutic molecule or molecules, or may include at least one mini-promoter cassette and a second cassette.
  • the second cassette may be a second mini-promoter cassette, a core-promoter cassette, an IRES cassette or a polIII promoter cassette.
  • a “core promoter” refers to a minimal promoter comprising about 50-100 bp and lacks enhancer elements.
  • core promoters include, but are not limited to, SCP1, AdML and CMV core promoters. More particularly, where a core-promoter cassette is present a second cassette (e.g ., a second mini-promoter cassette, a polIII promoter cassette or IRES cassette) will be present.
  • a vector comprising a cassette with a core promoter specifically excludes the use of SCP1, AdML and CMV core promoters, but rather utilize designer core promoters as described further herein and below.
  • Core promoters include certain viral promoters.
  • Viral promoters are promoters that have a core sequence but also usually some further accessory elements.
  • the early promoter for SV40 contains three types of elements: a TATA box, an initiation site and a GC repeat ( Barrera-Saldana et al., EMBO J, 4:3839-3849, 1985 ; Yaniv, Virology, 384:369-374, 2009 ).
  • the TATA box is located approximately 20 base-pairs upstream from the transcriptional start site.
  • the GC repeat regions is a 21 base-pair repeat containing six GC boxes and is the site that determines the direction of transcription. This core promoter sequence is around 100 bp.
  • Adding an additional 72 base-pair repeats, thus making it a "mini-promoter,” is useful as a transcriptional enhancer that increase the functionality of the promoter by a factor of about 10.
  • the SP1 protein interacts with the 21 bp repeats it binds either the first or the last three GC boxes. Binding of the first three initiates early expression, and binding of the last three initiates late expression.
  • the function of the 72 bp repeats is to enhance the amount of stable RNA and increase the rate of synthesis. This is done by binding (dimerization) with the AP1 (activator protein 1) to give a primary transcript that is 3' polyadenylated and 5' capped.
  • Other viral promoters such as the Rous Sarcom Virus (RSV), the HBV X gene promoter, and the Herpes Thymidine kinase core promoter can also be used as the basis for selection desired function.
  • RSV Rous Sarcom Virus
  • HBV X gene promoter the Herpe
  • a core promoter typically encompasses -40 to +40 relative to the +1 transcription start site ( Juven-Gershon and Kadonaga, Dev. Biol. 339:225-229, 2010 ), which defines the location at which the RNA polymerase II machinery initiates transcription.
  • RNA polymerase II interacts with a number of transcription factors that bind to DNA motifs in the promoter. These factors are commonly known as “general” or “basal” transcriptions factors and include, but are not limited to, TFIIA (transcription factor for RNA polymerase IIA), TFIIB, TFIID, TFIIE, TFIIF, and TFIIH. These factors act in a “general” manner with all core promoters; hence they are often referred to as the "basal” transcription factors.
  • the pRC/CMV core promoter consists of a TATA box and is 81 bp in length
  • the CMV core promoter consists of a TATA box and a initiator site
  • the SCP synthetic core promoters consist of a TATA box, an Inr (initiator), an MTE site (Motif Ten Element), and a DPE site (Down stream promoter element) and is about 81 bp in length.
  • the SCP synthetic promoter has improved expression compared to the simple pRC/CMV core promoter.
  • mini-promoter refers to a regulatory domain that promotes transcription of an operably linked gene or coding nucleic acid sequence.
  • the mini-promoter includes the minimal amount of elements necessary for effective transcription and/or translation of an operably linked coding sequence.
  • a mini-promoter can comprise a "core promoter” in combination with additional regulatory elements or a "modified core promoter”.
  • the mini-promoter or modified core promoter will be about 100-600 bp in length while a core promoter is typically less than about 100bp ( e.g., about 70-80 bp).
  • the cassette will typically comprise an enhancer element or another element either upstream or downstream of the core promoter sequence that facilitates expression of an operably linked coding sequence above the expression levels of the core promoter alone.
  • mini-promoters e . g., modified core promoters
  • core promoter elements ⁇ 100, ⁇ 200, ⁇ 400 or ⁇ 600 bp
  • mini-promoters comprising core promoters plus minimal enhancer sequences and/or Kozak sequences to allow better gene expression compared to a core-promoter lacking such sequences that are still under 200, 400 or 600bp.
  • mini-promoters include modified core promoters and naturally occurring tissue specific promoters such as the elastin promoter (specific for pancreatic acinar cells, (204 bp; Hammer et al., Mol Cell Biol., 7:2956-2967, 1987 ) and the promoter from the cell cycle dependent ASK gene from mouse and man (63-380 bp; Yamada et al., J. Biol. Chem., 277: 27668-27681, 2002 ).
  • tissue specific promoters such as the elastin promoter (specific for pancreatic acinar cells, (204 bp; Hammer et al., Mol Cell Biol., 7:2956-2967, 1987 ) and the promoter from the cell cycle dependent ASK gene from mouse and man (63-380 bp; Yamada et al., J. Biol. Chem., 277: 27668-27681, 2002 ).
  • Ubiquitously expressed small promoters also include viral promoters such as the SV40 early and late promoters (about 340 bp), the RSV LTR promoter (about 270 bp) and the HBV X gene promoter (about 180 bp) (e.g., R Anish et al., PLoS One, 4: 5103, 2009 ) that has no canonical "TATTAA box” and has a 13 bp core sequence of 5'-CCCCGTTGCCCGG-3' (SEQ ID NO:42).
  • the therapeutic cassette comprising at least one mini-promoter cassette will have expression levels that exceed, are about equal to, or about about 1 fold to 2.5 fold less than the expression levels of an IRES cassette present in an RRV.
  • Transcription from a core- or mini-promoter occurs through the interaction of various elements.
  • focused transcription for example, there is either a single major transcription start site or several start sites within a narrow region of several nucleotides. Focused transcription is the predominant mode of transcription in simpler organisms.
  • dispersed transcription there are several weak transcription start sites over a broad region of about 50 to 100 nucleotides. Dispersed transcription is the most common mode of transcription in vertebrates. For instance, dispersed transcription is observed in about two-thirds of human genes. In vertebrates, focused transcription tends to be associated with regulated promoters, whereas dispersed transcription is typically observed in constitutive promoters in CpG islands.
  • a mini-promoter used in the compositions of the disclosure can comprise a core promoter that is further modified. Such modifications can include the incorporation of one or more additional elments as set forth in Table 1.
  • Table 1 Binding sites that can contribute to a focused core promoter (almost always with a "TATA box and a single transcription start site (TSS)), or a dispersed promoter without a TATA box, usually with a DPE element (see R. Dickstein, Trasncription, 2(5):201-206, 2011; Juven-Gershon et al., Nat.
  • Transcription factor Full name Binding site wrt to transcription start site (TSS +1) BREu TFIIB recognition element, upstream Upstream of TATA Box, SSRCGCC TATA box TATA box T at -31/-30 TATAWAAR, key focused promoter element BREd TFIIB recognition element, downstream -23 to -17 RTDKKKK XCPE1 HBV X core promoter element 1 -8 to +2 DSGYGGRASM from HBV Xgene XCPE2 HBV X core promoter element 2 VCYCRTTRCMY from HBV Xgene Inr initiator -2 to +4 YYANWYY DCE SI Downstream core element site 1 +6 to +11 CTTC DCE SII Downstream core element site II +16 to +21 CTGT DCE S
  • Table 2 sets forth oligonucleotides that can be used to construct and clone enhancer elements into core promoter regions.
  • the modified/optimized core promoters of the disclosure can include a core sequence with the addition of elements from Table 1 and may further include enhancers cloned as set forth in Table 2. In doing so, the size of the core-promoter is increased and can be described as a "mini-promoter". However, the final mini-promoter should not exceed 600 bp and will typically be about 100 bp, 200 bp, 300 bp, 400 bp, 500 bp and any integer there between. Table 2. Oligonucleotides used for constructing enhancer segments. No.
  • Oligonucleotide Motif Sequence (SEQ ID NOs in Reference 1 AP-1 5'-TGTCTCAG-3' (43) Hallahan et al. Int. J. Radiat. Oncol. Biol. Phys. 36:355-360, 1996 2 CArG 5'-CCATATAAGG-3' (44) Datta et al. Proc. Natl. Acad. Sci. USA 89:10149-10153, 1992 3 NF- ⁇ B1 5'-GGAAATCCCC-3' (45) Ueda et al. FEBS Lett. 491:40-44, 2001 4 NF- ⁇ B2 5'-GGAAAGTCCCC-3' (46) Kanno et al. EMBO J.
  • the mini-promoter includes regulatory elements (e.g., Kozak sequences) that can improve translation of transcript mRNA.
  • Other "Kozak-like" sequences that can promote efficient translation are known in the art.
  • sequences derived from the 5'-UTR of tobacco mosaic virus mRNA as well as from the lobster tropomyosin gene are able to function in eukaryotic cells to enhance protein translation (Gallei et al., 1989, Gallei et al., 1992 and Gallei et al., 2002; Sano et al., 2002).
  • the length of these sequences varies from 7 to 68 nucleotides (see, e.g., Table 3).
  • Table 3 Known translational enhancer found in 5' UTR of coding genes.
  • the mini-promoter includes regulatory elements (e.g ., Kozak sequences) that can improve translation of transcript mRNA.
  • analysis of the sequence to be expressed and translated i.e ., the sequence to which the mini-promoter is operably linked
  • a heat-stabilized, humanized, yeast cytosine deaminase (yCD2) coding sequence has 3 in-frame ATG within the first 15 amino acids in the coding region.
  • the spacing in the 5'UTR and the lack of Kozak sequence flanking the initiation codon in yCD2 mRNA is suboptimal for efficient protein translation initiation.
  • incorporation of Kozak sequence and/or other translational enhancer element may greatly improve the translation initiation and thus protein production of transgenes.
  • the mini-promoters can comprise optimized or modified core promoters that include one or more additional elements that facilitate expression of an operably linked coding sequence.
  • One way of selecting for functional mixtures of these elements is to simply synthesize the various elements or variations of these elements, ligate them together and select functionally for mini-promoters that are able to express in the desired situation.
  • Juven-Gershon et al. describes assays which can be used to determine the expression levels of operably linked genes ( e.g ., using luciferase report constructs and the like).
  • NF- ⁇ B nuclear factor ⁇ B
  • CBF-A CArG binding factor A
  • NF-Y nuclear factor Y
  • functional enhancers Ogawa et al., Biotechniques, 42:628-633, 2007
  • a cellular core promoter for example, from the hemoxygenase core
  • other core promoters such as the SCP1 core, optimized core sequences as described here, the TK intragenic core ( Al-shawi et al., Mol. Cell.
  • DHFR dyhdrofolate reductase
  • a nucleotide transport inhibitor such as dipyridamole ( Warlick et al., Biochemical Pharmacology, 59: 141-151, 2000 ) or nitrobenzylmercaptopurine riboside phosphate ( Allay et al., Stem Cells, 16(suppl 1):223-233, 1998 ); Cytosine deaminase using N-(phosphonacetyl)-L-aspartate (PALA) to block de novo synthesis of uracil and anabolically downstream bases and cytosine to supply these through pyrimidine salvage pathways ( Wahl et al., J.
  • PHA N-(phosphonacetyl)-L-aspartate
  • modified or optimized promoters may be obtained through "directed evolution", error prone PCR and the like.
  • rounds of expression and selection can provide for the introduction of errors in a mini-promoter (e.g., a core promoter or modified core promoter) and selection of positive expression profiles using selectable systems such as the DHFR and CD selection schemes described above.
  • transgenes that are not sufficiently expressed using mini-promoters can be selected for increased expression in the context of an RRV by including a metabolically selectable gene in the RRV and passing the RRV through multiple rounds of replication and selection.
  • the relatively high error rate of the viral reverse transcriptase enzyme allows the incorporation of mutations and advantageous mutations are then selected and become the dominant sequence.
  • Such improved mini-promoters can then be amplified, cloned and used as a more efficient minipromoter.
  • the selection can be performed in tumor cell lines of a desired cell type, such as colon, brain, lung, breast or prostate cancers.
  • a desired cell type such as colon, brain, lung, breast or prostate cancers.
  • sequential passage of the RRV encoding the selectable marker driven by a putative minimal promoter in the presence of the selective agent leads to selection for the best expressing minimal promoter.
  • Passage of the RRV in tumor cell lines of the proposed target type can be used if there are tissue specificity issues with a particular combination.
  • the mini-promoter is synthesized as a single entity and the rate of error accumulation of the RRV reverse transcriptase is relied on to introduce diversity on which selection can be made.
  • the initial promoter is synthesized with programmed random inhomogeneities in the sequence so that when incorporated into the RRV as the promoter for the selectable marker, there is a larger landscape of possible sequences to to select from.
  • the initial viral vector can be supplied with random variants in the promoter sequence and the same type of selection can be used to identify optimal mini-promoter sequences.
  • Kozak sequence RCCATGG (SEQ ID NO:51) can be incorporated downstream of the mini promoters to facilitate the initial binding of the mRNA to the small subunit of the ribosome, thus improve translation.
  • Optimized mini-promoters with sufficient expression can be used in any situation where nucleic acid size is limiting (e.g., viral vectors).
  • the optimized mini-promoter is used in a replicating RRV to express one or more genes with an anticancer effect.
  • the mini-promoter is used to express two genes, either as a fusion, a fusion gene separated by a protease cleavage site such as the furin endogenous protease target, or separated by a self-processing sequence like the 2A family (de Felipe et al., Trends Biotech, 24:68-75, 2006 ) or by the inclusion of two mini-promoters, one for each gene.
  • the mini-promoter can be used to express a first gene or coding sequence and then a second cassette comprising a polIII promoter can be used to express an siRNA, shRNA or microRNA. Because the mini-promoter cassette is smaller, it can be effectively combined to incorporate other therapeutic coding sequences.
  • the mini-promoters described herein that are operably linked to a gene or coding sequence to be expressed can be used to drive transcription in a vector.
  • the disclosure provides vectors comprising from 5' to 3': a CMV-R-U5 fusion of the immediate early promoter from human cytomegalovirus to an MLV R-U5 region; a PBS, primer binding site for reverse transcriptase; a 5' splice site; ⁇ packaging signal; a gag coding sequence for MLV group specific antigen; a pol coding sequence for MLV polymerase polyprotein; a 3' splice site; a 4070A env coding sequence for envelope protein of MLV strain 4070A; a therapeutic cassette comprising (a) at least one mini-promoter cassettes operably linked to a therapeutic gene or (b) a core-promoter and at least one other cassette selected from the group consisting of a polIII promoter cassette, a second core-promoter cassette, a mini-
  • each of these various "portion" of the vector can comprise well known sequences in the art derived from various gamma retroviral vectors (e.g., MLV, GALV and the like).
  • the vector is derived from or engineered from an MLV viral sequence.
  • Figure 8A and 8B depict various vectors of the disclosure as described in more detail elsewhere herein.
  • the promoter at the 5' end of the vector can comprise a CMV promoter having a sequence as set forth in SEQ ID NO:19, 20 or 22 from nucleotide 1 to about nucleotide 582 and may include modification to one or more nucleic acid bases and which is capable of directing and initiating transcription.
  • the vector promoter comprises a sequence as set forth in SEQ ID NO: 19, 20 or 22 from nucleotide 1 to about nucleotide 582.
  • the promoter comprises a CMV-R-U5 domain polynucleotide.
  • the CMV-R-U5 domain comprises the immediately early promoter from human cytomegalovirus linked to an MLV R-U5 region.
  • the CMV-R-U5 domain polynucleotide comprises a sequence as set forth in SEQ ID NO: 19, 20 or 22 from about nucleotide 1 to about nucleotide 1202 or sequences that are at least 95% identical to a sequence as set forth in SEQ ID NO: 19, 20 or 22 from about nucleotide 1 to about 1202, wherein the polynucleotide promotes transcription of a nucleic acid molecule operably linked thereto.
  • the gag and pol genes of the vector are derived from an oncoretrovirus or gamma retrovirus.
  • the gag nucleic acid domain can comprise, for example, a sequence from about nucleotide number 1203 to about nucleotide 2819 of SEQ ID NO: 19 or 22 or a sequence having at least 95%, 98%, 99% or 99.8% identity thereto.
  • the pol domain can comprise a sequence from about nucleotide number 2820 to about nucleotide 6358 of SEQ ID NO: 19 or 22 or a sequence having at least 95%, 98%, 99% or 99.9% identity thereto.
  • the env domain encodes an amphotropic env protein.
  • the env domain can comprise a sequence from about nucleotide number 6359 to about nucleotide 8323 of SEQ ID NO: 19 or 22 or a sequence having at least 95%, 98%, 99% or 99.8% identity thereto.
  • a therapeutic cassette is located just downstream of the env termination codon. Typically the therapeutic cassette starts immediately after or about 1, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, or about 100 basepairs downstream of the env stop codon. The beginning of the therapeutic cassette will typically have a minimal distance from the env stop codon so as to optimize the size of the heterologous gene in the cassette.
  • the therapeutic cassette can comprise one or more mini-promoters each operably linked to a therapeutic coding sequences, or a mini-promoter and a polIII promoter each operably linked to a therapeutic coding sequences, or a mini-promoter and an IRES each operably linked to a therapeutic coding sequences.
  • the mini-promoter of the vector can be any regulatory domain that is smaller than 600 bp ( e.g., about 599 bp, 550 bp, 500 bp, 450 bp, 400 bp, 350 bp, 300 bp, 250 bp, 200 bp, 150 bp, 100 bp, about 90 bp, about 80 bp, about 76 bp, about 74 bp or smaller) and allows for transcription of an operably linked coding sequence or non-coding sequence.
  • 600 bp e.g., about 599 bp, 550 bp, 500 bp, 450 bp, 400 bp, 350 bp, 300 bp, 250 bp, 200 bp, 150 bp, 100 bp, about 90 bp, about 80 bp, about 76 bp, about 74 bp or smaller
  • the cassette comprises a core-promoter such as from about nucleotide number 8330 to about nucleotide 8406 of SEQ ID NO: 19 or 22 or a sequence having at least 95%, 98%, or 99% identity thereto.
  • the core-promoter set forth in SEQ ID NO:19 or 22 from about 8328 to 8404 can be substituted with any number of other core- or mini-promoters including the promoters having the sequences as set forth in SEQ ID NO:56, 57, 59, 65, 66, 67, 68, 69, 71, 72, 73, and 74 and may further include additional sequences such as enhancer ( e.g., SEQ ID NO:58 and 70).
  • SEQ ID NO:19 depicts a pAC3-C1.yCD2 vector wherein the vector comprises a gag, pol and env sequence, the env sequence immediately followed by a CMV core promoter and a humanized cytosine deaminase with 3 heat stabilized mutation, which is then followed by the 3' LTR.
  • SEQ ID NO:20 depicts a similar structure however, the cassette comprises an S1 promoter followed by the transgene of human GMCSF.
  • SEQ ID NO:21 shows the sequence of a prior art RRV vector "pACE-CD".
  • SEQ ID NO:22 shows a sequence similar to SEQ ID NO:19 and 20 expect the promoter cassette comprises an S1 promoter operably linked to murine GMCSF.
  • SEQ ID NO:39 shows the sequence of an RRV having an S1-yCD2 cassette.
  • SEQ ID NO:40 shows the sequence of an RRV having a C1-GFP cassette.
  • SEQ ID NO:41 shows the sequence of an RRV having an S1-GFP cassette.
  • express and expression mean allowing or causing the information in a gene or DNA sequence to become manifest, for example producing a protein by activating the cellular functions involved in transcription and translation of a corresponding gene or DNA sequence.
  • a DNA sequence is expressed in or by a cell to form an "expression product” such as a protein.
  • the expression product itself e.g. the resulting protein, may also be said to be “expressed” by the cell.
  • a polynucleotide or polypeptide is expressed recombinantly, for example, when it is expressed or produced in a foreign host cell under the control of a foreign or native promoter, or in a native host cell under the control of a foreign promoter.
  • vectors comprising a core- or mini-promoter
  • other "vectors” can includes such core- or mini-promoter constructs to express operably linked genes and sequences.
  • vector means the vehicle by which a DNA or RNA sequence (e.g., a foreign gene) can be introduced into a host cell, so as to transform the host and promote expression (e.g., transcription and translation) of the introduced sequence.
  • Vectors typically comprise the DNA of a transmissible agent, into which foreign DNA encoding a protein is inserted by restriction enzyme technology.
  • a common type of vector is a "plasmid", which generally is a self-contained molecule of double-stranded DNA that can readily accept additional (foreign) DNA and which can readily introduced into a suitable host cell.
  • plasmid a vector that can readily accept additional (foreign) DNA and which can readily introduced into a suitable host cell.
  • vectors including plasmid and fungal vectors, have been described for replication and/or expression in a variety of eukaryotic and prokaryotic hosts.
  • most vectors have particular size limitations on what can be cloned into the vector (e.g., 12kb for plasmids, 20 kb for lambda bacteriophage, 30-35 kb for cosmids). This is even more restrictive when one considers retroviral vectors.
  • the genome of a typical replication-competent murine retrovirus is about 8.3 kb, whereas that of the alpha retrovirus RSV, which contains a disposable src sequences in addition to the normal complement of viral genes, is about 9.3 kb.
  • the maximum size for a replication-competent spleen necrosis virus vector is similar, about 10 kb ( Gelinas and Temin 1986) (Retroviruses., Coffin JM, Hughes SH, Varmus HE, editors., Cold Spring Harbor (NY): Cold Spring Harbor Laboratory Press; 1997 ).
  • the size limit on the retroviral genome depends on the size of the folded dimeric RNA.
  • "gutted" or replication defective retroviral vectors can incorporate larger sequence than their replication competent counter parts.
  • the disclosure provides retroviral replicating vectors that contain a heterologous polynucleotide encoding, for example, a polypeptide having cytosine deaminase or mutant thereof; a polypeptide having thymidine kinase activity or mutants thereof; other prodrug activating genes; an microRNA, shRNA or siRNA; a cytokine; an antibody binding domain or combinations thereof that can be delivered to a cell or subject.
  • a heterologous polynucleotide encoding for example, a polypeptide having cytosine deaminase or mutant thereof; a polypeptide having thymidine kinase activity or mutants thereof; other prodrug activating genes; an microRNA, shRNA or siRNA; a cytokine; an antibody binding domain or combinations thereof that can be delivered to a cell or subject.
  • retroviral vectors other viral vector that can be used in the compositions and methods of the disclosure and which can be engineered to contain a core- or mini-prmoter cassette include adenoviral vectors, a measles vectors, a herpes vectors, a retroviral vectors (including a lentiviral vector), a rhabdoviral vectors such as a Vesicular Stomatitis viral vectors, a reovirus vectors, a Seneca Valley Virus vectors, a poxvirus vectors (including animal pox or vaccinia derived vectors), a parvovirus vectors (including an AAV vectors), an alphavirus vectors or other viral vector known to one skilled in the art (see also, e.g., Concepts in Genetic Medicine, ed.
  • the disclosure provides modified retroviral vectors.
  • the modified retroviral vectors can be derived from members of the retroviridae family. Retroviruses have been classified in various ways, but the nomenclature has been standardized in the last couple of decades (see ICTVdB - The Universal Virus Database, 2012 release, on the World Wide Web (www) at ncbi.nlm.nih.gov/ICTVdb/ICTVdB/ and the text book “Retroviruses” Eds Coffin, Hughs and Varmus, Cold Spring Harbor Press 1997 ; the disclosures of which are incorporated herein by reference).
  • the retroviral replicating vector can comprise an Orthoretrovirus or more typically a gamma retrovirus vector.
  • a retroviral replicating vector therapeutically, it is advantageous to have high levels of expression of the transgene that is encoded by the retroviral replicating vector.
  • a prodrug activating gene such as the cytosine deaminase gene it is advantageous to have higher levels of expression of the CD protein in a cell so that the conversion of the prodrug 5-FC to 5-FU is more efficient.
  • high levels of expression of siRNA or shRNA lead to more efficient suppression of target gene expression.
  • cytokines or single chain antibodies (scAbs) or binding portion of an antibody it is usually advantageous to express high levels of the cytokine or scAb.
  • the disclosure provides recombinant replication competent retroviruses capable of infecting a target cell or target cell population multiple times resulting in an average number of copies/diploid genome of 3 or greater.
  • the disclosure also provides methods of testing for this property. Also provided are methods of treating a cell proliferative disorder, using a retroviral replicating vector capable of infecting a target cell or target cell population multiple times resulting in an average number of copies/diploid genome of 5 or greater.
  • the disclosure provides a recombinant retrovirus capable of infecting a non-dividing call, a dividing cell, or a cell having a cell proliferative disorder.
  • the recombinant replication competent retrovirus of the disclosure comprises a polynucleotide sequence encoding a viral GAG, a viral POL, a viral ENV, a therapeutic cassette comprising at least one heterologous polynucleotide preceded by a core- or mini-promoter, encapsulated within a virion.
  • non-dividing cell refers to a cell that does not go through mitosis. Non-dividing cells may be blocked at any point in the cell cycle, ( e.g ., G 0 /G 1 , G 1/S , G 2/M ), as long as the cell is not actively dividing. For dividing cells ortho- or gamma-retroviral vectors can be used.
  • dividing cell By “dividing" cell is meant a cell that undergoes active mitosis, or meiosis. Such dividing cells include stem cells, skin cells (e.g., fibroblasts and keratinocytes), gametes, and other dividing cells known in the art. Of particular interest and encompassed by the term dividing cell are cells having cell proliferative disorders, such as neoplastic cells.
  • cell proliferative disorder refers to a condition characterized by an abnormal number of cells.
  • the condition can include both hypertrophic (the continual multiplication of cells resulting in an overgrowth of a cell population within a tissue) and hypotrophic (a lack or deficiency of cells within a tissue) cell growth or an excessive influx or migration of cells into an area of a body.
  • the cell populations are not necessarily transformed, tumorigenic or malignant cells, but can include normal cells as well.
  • Cell proliferative disorders include disorders associated with an overgrowth of connective tissues, such as various fibrotic conditions, including scleroderma, arthritis and liver cirrhosis.
  • Cell proliferative disorders include neoplastic disorders such as head and neck carcinomas, squamous cell cancer, malignant melanoma, sinonasal undifferentiated carcinoma (SNUC), brain (including glioblastomas), blood neoplasia, carcinoma's of the regional lymph nodes, lung cancer, colon-rectum cancer, breast cancer, prostate cancer, urinary tract cancer, uterine cancer lymphoma, oral cancer, pancreatic cancer, leukemia, melanoma, stomach cancer, skin cancer and ovarian cancer (see, e.g., DeVita, Hellman, and Rosenberg's Cancer: Principles and Practice of Oncology 9th edition 2011 Wolters Kluwer/Lippincott Williams & Williams for descriptions of these various neoplasia and their current treatments).
  • neoplastic disorders such as head and neck carcinomas, squamous cell cancer, malignant melanoma, sinonasal undifferentiated carcinoma (SNUC), brain (including
  • the cell proliferative disease also includes rheumatoid arthritis ( O'Dell NEJM 350:2591 2004 )and other auto-immune disorders ( Mackay et al NEJM 345:340 2001 ) that are often characterized by inappropriate proliferation of cells of the immune system.
  • the vector of the disclosure (e.g., an RRV vector) comprises a core- and/or mini-promoter cassette operably linked to a heterologous nucleic acid sequence.
  • a heterologous nucleic acid sequence or transgene refers to (i) a sequence that does not normally exist in a wild-type retrovirus, (ii) a sequence that originates from a foreign species, or (iii) if from the same species, it may be substantially modified from its original form.
  • an unchanged nucleic acid sequence that is not normally expressed in a cell is a heterologous nucleic acid sequence.
  • any number of heterologous polynucleotide or nucleic acid sequences may be inserted into the retroviral vector. Additional polynucleotide sequences encoding any desired polypeptide sequence may also be inserted into the vector of the disclosure. Where in vivo delivery of a heterologous nucleic acid sequence is sought both therapeutic and non-therapeutic sequences may be used.
  • the heterologous sequence can encode a therapeutic molecule including an inhibitory nucleic acid molecule (microRNA, shRNA siRNA) or ribozymes directed to a particular gene associated with a cell proliferative disorder or other gene-associated disease or disorder;
  • the heterologous sequence can be a suicide gene (e.g., HSV-tk or PNP or cytosine deaminase; either modified or unmodified), a growth factor or a therapeutic protein (e.g ., Factor IX, IL2, GMCSF and the like) and any combination thereof.
  • suicide gene e.g., HSV-tk or PNP or cytosine deaminase; either modified or unmodified
  • a growth factor or a therapeutic protein e.g ., Factor IX, IL2, GMCSF and the like
  • Other therapeutic proteins or coding sequences applicable to the disclosure are easily identified in the art.
  • the heterologous polynucleotide within the vector comprises a cytosine deaminase that has been optimized for expression in a human cell (see, e.g., SEQ ID NO:3 and 5).
  • the cytosine deaminase comprises a sequence that has been human codon optimized and comprises mutations that increase the cytosine deaminase's stability (e.g., reduced degradation or increased thermo-stability) compared to a wild-type cytosine deaminase (see, e.g., SEQ ID NO:3).
  • the heterologous polynucleotide encodes a fusion construct comprising a cytosine deaminase (either human codon optimized or non-optimized, either mutated or non-mutated) operably linked to a polynucleotide encoding a polypeptide having UPRT or OPRT activity.
  • the heterologous polynucleotide comprises a CD polynucleotide of the disclosure ( e.g., SEQ ID NO:3, 5, 11, 13, 15, or 17).
  • the heterologous polynucleotide is a human codon optimized sequence encoding a polypeptide having thymidine kinase activity (see, e.g., SEQ ID NO:75).
  • a vector of the disclosure e.g., an RRV
  • a vector of the disclosure can comprise a heterologous polynucleotide encoding a polypeptide comprising a cytosine deaminase activity and may further comprise a polynucleotide comprising a microRNA or siRNA molecule either as part of the primary transcript from the viral promoter or linked to a promoter, which can be cell-type or tissue specific.
  • the disclosure provides a recombinant retroviral replicating vector that contains a heterologous polynucleotide sequence of the human primary precursor miR-128-2 (SEQ ID NO:32) downstream of the env gene. miRNAs that are down-regulated in cancers can be incorporated into the vector for therapeutic gene delivery.
  • let-7 miR-26, miR-124, miR181, MiR181d and miR-137 ( Esquela-Kerscher et al., 2008 Cell Cycle 7, 759-764 ; Kumar et al., 2008 Proc Natl Acad Sci USA 105, 3903-3908 ; Kota et al., 2009 Cell 137, 1005-1017 ; Silber et al., 2008 BMC Medicine 6:14 1-17 ).
  • the replicating retroviral vectors of the disclosure can be used to treat disease by expressing engineered siRNA, shRNA or miRNA ( Dennis, Nature, 418: 122 2002 ) that switches off or lowers expression of key genes that govern the proliferation or survival of diseased cells including tumor cells.
  • engineered siRNA, shRNA or miRNA Dennis, Nature, 418: 122 2002
  • Such targets include genes like Rad 51 a central enzyme in DNA repair, and without which cell growth is drastically restricted.
  • Other targets include many of the signaling pathway molecules that control cell growth ( Marquez & McCaffrey Hum Gene Ther. 19:27 2008 ) or inhibit viral replication ( WE Johnson Current Topics in Microbiology and Immunology 371: 123-151, 2013 ) such as APOBEC3G or tetherin.
  • the siRNA or miRNA may be combined with expression of a cytotoxic gene from the same or different retroviral vector of the disclosure.
  • An example of a suitable cytotoxic gene comprises a cytosine deaminase or modified cytosine deaminase of the disclosure.
  • Examples of siRNA or miRNA that can be expressed from the same vector or a different vector with cytosine deaminase are siRNAs or miRNAs that target thymidilate synthase, dihydropyrimidine dehydrogenase or other nucleic acid anabolic or synthetic enzymes, that can enhance or complement the action of 5-FU produced locally in a tumor or tissue from 5-FC activation by cytosine deaminase.
  • the RRV will comprise a therapeutic cassette having a core- or mini-promoter operably linked to a sequence encoding a polypeptide with CD activity and further includes a polIII promoter cassette operably linked to a sequence the encodes an miRNA.
  • the retroviral vector(s) will replicate through the tumor or other target tissue and before growth inhibition occurs the virus first integrates into the host genome and continues to make virus after growth of that cell is inhibited.
  • Methods for selecting functional miRNA or siRNA sequences are known in the art.
  • a retroviral vector of this disclosure can be made using cells from other species for which the corresponding protein is not significantly targeted. Such cells include dog cell lines or chicken cell line.
  • the virus is made by transient transfection on human 293 derived cells or other cell line that allows efficient transient transfection.
  • the siRNA or miRNA sequence can simply be inserted at a convenient site on the viral genome. This site includes the region downstream of the envelope and upstream of the 3'LTR of the replicating retrovirus.
  • polIII transcription units can be inserted in the viral genome with the appropriate siRNA or miRNA, typically downstream of the 3' envelope gene.
  • the transcription direction will be the same as that of the retroviral replicating vector.
  • siRNA or miRNA sequences can be inserted to ensure efficient down regulation of the target gene or down regulation of more than one gene.
  • RNAi resources including siRNA and shRNA design tools. (Hannon Lab, Cold Spring Harbor Laboratory); http:(//)www.rnaiweb.com/ General resource; http:(//)genomics.jp/ sidirect/; http:(//)[www].rnainterference.org/; http:(//)bioinfo. wistar.upenn.edu/siRNA /siRNA.htm; http:(//)www(.)ambion.com/ techlib/misc/ siRNA_finder.html (Ambion)).
  • the miRNA target can be inserted 3' to the transgene but before the 3'LTR or upstream of the mini-promoter in the therapeutic cassette but after the 3' end of the envelope. In general the target would not be inserted into protein coding sequences.
  • the heterologous polynucleotide may comprise a cytokine such as an interleukin, interferon gamma or the like.
  • Cytokines that may expressed from a retroviral vector of the disclosure include, but are not limited to, IL-1alpha, IL-1beta, IL-2 (SEQ ID NO:38), IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12, IL-13, IL-14, IL-15, IL-16, IL-17, IL-18, IL-19, IL-20, and IL-21, anti-CD40, CD40L, IFN-gamma (SEQ ID NO:36, 37, 38) and TNF-alpha, soluble forms of TNF-alpha, lymphotoxin-alpha (LT-alpha, also known as TNF-beta), LT-beta (found in complex heterotrimer LT-al
  • WO 96/14328 AIM-I (International Publication No. WO 97/33899 ), endokine-alpha (International Publication No. WO 98/07880 ), OPG, and neutrokine-alpha (International Publication No. WO 98/18921 , OX40, and nerve growth factor (NGF), and soluble forms of Fas, CD30, CD27, CD40 and 4-IBB, TR2 (International Publication No. WO 96/34095 ), DR3 (International Publication No. WO 97/33904 ), DR4 (International Publication No. WO 98/32856 ), TR5 (International Publication No. WO 98/30693 ), TRANK, TR9 (International Publication No.
  • WO 98/56892 discloses a wide range of diseases and conditions in which TRIO (International Publication No. WO 98/54202 ), 312C2 (International Publication No. WO 98/06842 ), and TR12, and soluble forms CD154, CD70, and CD153.
  • Angiogenic proteins may be useful in some embodiments, particularly for protein production from cell lines.
  • angiogenic factors include, but are not limited to, Glioma Derived Growth Factor (GDGF), Platelet Derived Growth Factor-A (PDGF-A), Platelet Derived Growth Factor-B (PDGF-B), Placental Growth Factor (PIGF), Placental Growth Factor-2 (PIGF-2), Vascular Endothelial Growth Factor (VEGF), Vascular Endothelial Growth Factor-A (VEGF-A), Vascular Endothelial Growth Factor-2 (VEGF-2), Vascular Endothelial Growth Factor B (VEGF-3), Vascular Endothelial Growth Factor B-1 86 (VEGF-B186), Vascular Endothelial Growth Factor-D (VEGF-D), Vascular Endothelial Growth Factor-D (VEGF-D), and Vascular Endothelial Growth Factor-E (VEGF-E).
  • GDGF Glioma Derived Growth Factor
  • PDGF-A Platelet Derived Growth Fact
  • Fibroblast Growth Factors may be delivered by a vector of the disclosure and include, but are not limited to, FGF-1, FGF-2, FGF-3, FGF-4, FGF-5, FGF-6, FGF-7, FGF-8, FGF-9, FGF-10, FGF-11, FGF-12, FGF-13, FGF-14, and FGF-15.
  • Hematopoietic growth factors may be delivered using vectors of the disclosure, such growth factors include, but are not limited to, granulocyte macrophage colony stimulating factor (GM-CSF) (sargramostim), granulocyte colony stimulating factor (G-CSF) (filgrastim), macrophage colony stimulating factor (M-CSF, CSF-1) erythropoietin (epoetin alfa), stem cell factor (SCF, c-kit ligand, steel factor), megakaryocyte colony stimulating factor, PIXY321 (a GMCSF/IL-3) fusion protein and the like.
  • GM-CSF granulocyte macrophage colony stimulating factor
  • G-CSF granulocyte colony stimulating factor
  • M-CSF macrophage colony stimulating factor
  • CSF-1 erythropoietin
  • SCF stem cell factor
  • c-kit ligand steel factor
  • megakaryocyte colony stimulating factor PIXY321 (
  • compositions of the disclosure are useful in combination therapies including therapies with other approved drugs or biologics such as Avastin, Herceptin or various HDAC inhibitors.
  • the disclosure provides methods for treating cell proliferative disorders such as cancer and neoplasms comprising administering an RRV vector of the disclosure followed by treatment with a chemotherapeutic agent or anti-cancer agent.
  • the RRV vector is administered to a subject for a period of time prior to administration of the chemotherapeutic or anti-cancer agent that allows the RRV to infect and replicate.
  • the subject is then treated with a chemotherapeutic agent or anti-cancer agent for a period of time and dosage to reduce proliferation or kill the cancer cells.
  • the subject may then be treated with a benign therapeutic agent (e.g ., 5-FC) that is converted to a toxic therapeutic agent in cells expression a cytotoxic gene (e.g ., cytosine deaminase) from the RRV.
  • a benign therapeutic agent e.g ., 5-FC
  • a cytotoxic gene e.g ., cytosine deaminase
  • the RRVs of the disclosure are spread during a replication process of the tumor cells, such cells can then be killed by treatment with an anti-cancer or chemotherapeutic agent and further killing can occur using the RVV treatment process described herein.
  • the heterologous gene can comprise a coding sequence for a target antigen (e.g., a cancer antigen).
  • a target antigen e.g., a cancer antigen
  • cells comprising a cell proliferative disorder are infected with an RRV comprising a heterologous polynucleotide encoding the target antigen to provide expression of the target antigen (e.g., overexpression of a cancer antigen).
  • An anticancer agent comprising a targeting cognate moiety that specifically interacts with the target antigen is then administered to the subject.
  • the targeting cognate moiety can be operably linked to a cytotoxic agent or can itself be an anticancer agent.
  • the blockading molecules are antibodies, single chain antibodies, soluble versions of the natural ligand or other peptides that bind such receptors.
  • the blocking targets are various surface molecules that include molecules involved in accessory immune interactions other than CTLA-4, but know to those skilled in the art.
  • the disclosure includes various pharmaceutical compositions useful for treating a cell proliferative disorder.
  • the pharmaceutical compositions according to the disclosure are prepared by bringing a retroviral vector containing a heterologous polynucleotide sequence useful in treating or modulating a cell proliferative disorder according to the disclosure into a form suitable for administration to a subject using carriers, excipients and additives or auxiliaries. Further information on the use of such strategies with RRV with smaller single genes is available in WO2010/036986 , WO2010/045002 , WO2011/126864 and WO2012/058673 and are similar for the vectors of this disclosure.
  • a retroviral vector useful in treating a cell proliferative disorder will include an amphotropic ENV protein, GAG, and POL proteins, a promoter sequence in the U3 region retroviral genome, and all cis-acting sequence necessary for replication, packaging and integration of the retroviral genome into the target cell.
  • a vector of the disclosure can comprise a core- and/or mini-promoter cassette and can further includes an IRES cassette.
  • An internal ribosome entry sites (“IRES"", Pelletier et al., 1988, Mol. Cell. Biol., 8, 1103-1112 ; Jang et al., J. Virol., 1988, 62, 2636-2643 ) refers to a segment of nucleic acid that promotes the entry or retention of a ribosome during translation of a coding sequence usually 3' to the IRES.
  • the IRES may comprise a splice acceptor/donor site, however, preferred IRESs lack a splice acceptor/donor site.
  • the therapeutic cassette can comprise a mini-promoter followed further 3' to the promoter by an IRES.
  • an RRV of the disclosure comprises a promoter region at the 5' end of the retroviral polynucleotide sequence.
  • the term "promoter region" is used herein in its ordinary sense to refer to a nucleotide region comprising a DNA regulatory sequence, wherein the regulatory sequence is derived from a gene which is capable of binding RNA polymerase and initiating transcription of a downstream (3'-direction) coding sequence.
  • the regulatory sequence may be homologous or heterologous to the desired gene sequence.
  • a wide range of promoters may be utilized, including viral or mammalian promoter as described above. Further information on the use of such strategies with RRV with smaller single genes is available in WO2010/036986 , WO2010/045002 , WO2011/126864 and WO2012/058673 and are similar for the vectors of this disclosure.
  • the retroviral genome of the disclosure contains mini-promoter comprising a cloning site downstream of the mini-promoter for insertion of a desired/heterologous polynucleotide in operaly frame to effectuate expression of the heterologous polynucleotide.
  • at least one mini-promoter is located 3' to the env gene in the retroviral vector, but 5' to the desired heterologous polynucleotide. Accordingly, a heterologous polynucleotide encoding a desired polypeptide may be operably linked to the mini-promoter.
  • a recombinant retrovirus of the disclosure is genetically modified in such a way that the virus is targeted to a particular cell type (e.g., smooth muscle cells, hepatic cells, renal cells, fibroblasts, keratinocytes, mesenchymal stem cells, bone marrow cells, chondrocyte, epithelial cells, intestinal cells, mammary cells, neoplastic cells, glioma cells, neuronal cells and others known in the art) such that the recombinant genome of the retroviral vector is delivered to a target non-dividing, a target dividing cell, or a target cell having a cell proliferative disorder.
  • a particular cell type e.g., smooth muscle cells, hepatic cells, renal cells, fibroblasts, keratinocytes, mesenchymal stem cells, bone marrow cells, chondrocyte, epithelial cells, intestinal cells, mammary cells, neoplastic cells, glioma cells
  • the targeting of the vector is achieved using a chimeric env protein comprising a retroviral ENV protein operably linked to a targeting polypeptide.
  • the targeting polypeptide can be a cell specific receptor molecule, a ligand for a cell specific receptor, an antibody or antibody fragment to a cell specific antigenic epitope or any other ligand easily identified in the art which is capable of binding or interacting with a target cell.
  • Examples of targeting polypeptides or molecules include bivalent antibodies using biotin-streptavidin as linkers ( Etienne-Julan et al., J. Of General Virol., 73, 3251-3255, 1992 ; Roux et al., Proc. Natl. Acad.
  • SNV spleen necrosis virus
  • the disclosure provides retroviral vectors that are targeted using regulatory sequences.
  • Cell- or tissue-specific regulatory sequences e.g., promoters
  • Suitable mammalian and viral promoters for the disclosure are described elsewhere herein.
  • the disclosure provides a retrovirus having tissue-specific promoter elements at the 5' end of the retroviral genome.
  • the tissue-specific regulatory elements/sequences are in the U3 region of the LTR of the retroviral genome, including for example cell- or tissue-specific promoters and enhancers to neoplastic cells (e.g., tumor cell-specific enhancers and promoters), and inducible promoters (e.g ., tetracycline).
  • cell- or tissue-specific promoters and enhancers to neoplastic cells e.g., tumor cell-specific enhancers and promoters
  • inducible promoters e.g ., tetracycline
  • Transcription control sequences of the disclosure can also include naturally occurring transcription control sequences naturally associated with a gene encoding a superantigen, a cytokine or a chemokine.
  • CMV immediate early promoter if often used to provide strong transcriptional activation.
  • Modified versions of the CMV promoter that are less potent have also been used when reduced levels of expression of the transgene are desired.
  • retroviral promoters such as the LTRs from MLV or MMTV can be used.
  • viral promoters that can be used include SV40, RSV LTR, HIV-1 and HIV-2 LTR, adenovirus promoters such as from the E1A, E2A, or MLP region, AAV ITR, cauliflower mosaic virus, HSV-TK, and avian sarcoma virus.
  • tissue specific or selective promoters may be used to effect transcription in specific tissues or cells so as to reduce potential toxicity or undesirable effects to non-targeted tissues.
  • promoters such as the PSA, probasin, prostatic acid phosphatase or prostate-specific glandular kallikrein (hK2) may be used to target gene expression in the prostate.
  • the Whey accessory protein (WAP) may be used for breast tissue expression ( Andres et al., PNAS 84:1299-1303, 1987 ).
  • tissue-specific regulatory elements are regulatory elements (e.g., promoters) that are capable of driving transcription of a gene in one tissue while remaining largely “silent” in other tissue types. It will be understood, however, that tissue-specific promoters may have a detectable amount of "background” or “base” activity in those tissues where they are silent.
  • the degree to which a promoter is selectively activated in a target tissue can be expressed as a selectivity ratio (activity in a target tissue/activity in a control tissue).
  • a tissue specific promoter useful in the practice of the disclosure typically has a selectivity ratio of greater than about 5. Preferably, the selectivity ratio is greater than about 15.
  • RRV retroviral replicating vector of the disclosure
  • promoters that are hormone or cytokine regulatable include MMTV, MT-1, ecdysone and RuBisco.
  • Other hormone regulated promoters such as those responsive to thyroid, pituitary and adrenal hormones may be used.
  • tissue specific promoters While not restricted in activity to a single tissue type, may nevertheless show selectivity in that they may be active in one group of tissues, and less active or silent in another group. Such promoters are also termed "tissue specific", and are contemplated for use with the disclosure. For example, promoters that are active in a variety of central nervous system (CNS) neurons may be therapeutically useful in protecting against damage due to stroke, which may affect any of a number of different regions of the brain. Accordingly, the tissue-specific regulatory elements used in the disclosure, have applicability to regulation of the heterologous proteins as well as a applicability as a targeting polynucleotide sequence in the present retroviral vectors.
  • CNS central nervous system
  • the retroviral vectors and methods of the disclosure provide a replication competent retrovirus that does not require helper virus or additional nucleic acid sequence or proteins in order to propagate and produce virion.
  • the nucleic acid sequences of the retrovirus of the disclosure encode a group specific antigen and reverse transcriptase, (and integrase and protease-enzymes necessary for maturation and reverse transcription), respectively, as discussed above.
  • the viral gag and pol can be derived from a lentivirus, such as HIV or an oncovirus or gammaretrovirus such as MoMLV.
  • the nucleic acid genome of the retrovirus of the disclosure includes a sequence encoding a viral envelope (ENV) protein.
  • the env gene can be derived from any retroviruses or other virus.
  • the env may be an amphotropic envelope protein which allows transduction of cells of human and other species, or may be an ecotropic envelope protein, which is able to transduce only mouse and rat cells.
  • the env gene is derived from a non-retrovirus (e.g ., CMV or VSV).
  • retroviral-derived env genes include, but are not limited to: Moloney murine leukemia virus (MoMuLV), Harvey murine sarcoma virus (HaMuSV), murine mammary tumor virus (MuMTV), gibbon ape leukemia virus (GaLV), human immunodeficiency virus (HIV) and Rous Sarcoma Virus (RSV).
  • Other env genes such as Vesicular stomatitis virus (VSV) (Protein G), cytomegalovirus envelope (CMV), or influenza virus hemagglutinin (HA) can also be used.
  • VSV Vesicular stomatitis virus
  • CMV cytomegalovirus envelope
  • HA influenza virus hemagglutinin
  • the retroviral genome is derived from an onco-retrovirus, and more particularly a mammalian onco-retrovirus.
  • the retroviral genome is derived from a gamma retrovirus, and more particularly a mammalian gamma retrovirus.
  • derived is meant that the parent polynucleotide sequence is a wild-type oncovirus which has been modified by insertion or removal of naturally occurring sequences (e.g ., insertion of mini-promoter, insertion of a heterologous polynucleotide encoding a polypeptide or inhibitory nucleic acid of interest, swapping of a more effective promoter from a different retrovirus or virus in place of the wild-type promoter and the like).
  • naturally occurring sequences e.g insertion of mini-promoter, insertion of a heterologous polynucleotide encoding a polypeptide or inhibitory nucleic acid of interest, swapping of a more effective promoter from a different retrovirus or virus in place of the wild-type promoter and the like.
  • the disclosure provides a retrovirus that is replication-competent.
  • the disclosure provides plasmids comprising a recombinant retroviral derived construct.
  • the plasmid can be directly introduced into a target cell or a cell culture such as NIH 3T3 or other tissue culture cells. The resulting cells release the retroviral vector into the culture medium.
  • host cells transfected with a retroviral replicating vector of the disclosure include eukaryotic cells such as yeast cells, insect cells, or animal cells. Host cells also include prokaryotic cells such as bacterial cells.
  • engineered host cells that are transduced (transformed or transfected) with a vector provided herein (e.g., a retroviral replicating vector).
  • the engineered host cells can be cultured in conventional nutrient media modified as appropriate for activating promoters, selecting transformants, or amplifying a coding polynucleotide. Culture conditions, such as temperature, pH and the like, are those previously used with the host cell selected for expression, and will be apparent to those skilled in the art and in the references cited herein, including, e.g., Freshney (1994) Culture of Animal Cells: A Manual of Basic Technique, 3rd ed.
  • Such host cells can also be used for delivery of RRV by administering the infected cells to an animal or subject (e.g., a patient).
  • Examples of appropriate expression hosts include: bacterial cells, such as E. coli, B. subtilis, Streptomyces, and Salmonella typhimurium; fungal cells, such as Saccharomyces cerevisiae, Pichia pastoris, and Neurospora crassa; insect cells such as Drosophila and Spodoptera frugiperda; mammalian cells such as CHO, COS, BHK, HEK 293 br Bowes melanoma; or plant cells or explants, etc.
  • bacterial cells such as E. coli, B. subtilis, Streptomyces, and Salmonella typhimurium
  • fungal cells such as Saccharomyces cerevisiae, Pichia pastoris, and Neurospora crassa
  • insect cells such as Drosophila and Spodoptera frugiperda
  • mammalian cells such as CHO, COS, BHK, HEK 293 br Bowes melanoma
  • the disclosure provides a polynucleotide construct comprising from 5' to 3': a promoter or regulatory region useful for initiating transcription; a psi packaging signal; a gag encoding nucleic acid sequence, a pol encoding nucleic acid sequence; an env encoding nucleic acid sequence; a therapeutic cassette comprising (a) a core-promoter and at least one addition promoter, each operably linked to a therapeutic polynucleotide sequence or (b) at least one mini-promoter operably linked to a heterologous polynucleotide encoding a marker, therapeutic or diagnostic polypeptide; and a LTR nucleic acid sequence.
  • the various segment of the polynucleotide construct of the disclosure e.g., a recombinant replication competent retroviral polynucleotide
  • a replication competent retroviral construct of the disclosure can be divided up into a number of domains that may be individually modified by those of skill in the art.
  • the viral promoter can comprise a CMV promoter having a sequence as set forth in SEQ ID NO:19, 20 or 22 from nucleotide 1 to about nucleotide 582 and may include modification to one or more ( e.g., 2-5, 5-10, 10-20, 20-30, 30-50, 50-100 or more nucleic acid bases) so long as the modified promoter is capable of directing and initiating transcription.
  • the promoter or regulatory region comprises a CMV-R-U5 domain polynucleotide.
  • the CMV-R-U5 domain comprises the immediately early promoter from human cytomegalovirus to the MLV R-U5 region.
  • the CMV-R-U5 domain polynucleotide comprises a sequence as set forth in SEQ ID NO:19, 20 or 22 from about nucleotide 1 to about nucleotide 1202 or sequences that are at least 95% identical to a sequence as set forth in SEQ ID NO:19, 20, or 22 wherein the polynucleotide promotes transcription of a nucleic acid molecule operably linked thereto.
  • the gag domain of the polynucleotide may be derived from any number of retroviruses, but will typically be derived from an oncoretrovirus and more particularly from a mammalian oncoretrovirus.
  • the gag domain comprises a sequence from about nucleotide number 1203 to about nucleotide 2819 or a sequence having at least 95%, 98%, 99% or 99.8% (rounded to the nearest 10 th ) identity thereto.
  • the pol domain of the polynucleotide may be derived from any number of retroviruses, but will typically be derived from an oncoretrovirus and more particularly from a mammalian oncoretrovirus.
  • the pol domain comprises a sequence from about nucleotide number 2820 to about nucleotide 6358 or a sequence having at least 95%, 98%, 99% or 99.9% (rounded to the nearest 10 th ) identity thereto.
  • the env domain of the polynucleotide may be derived from any number of retroviruses, but will typically be derived from an oncoretrovirus or gamma-retrovirus and more particularly from a mammalian oncoretrovirus or gamma-retrovirus.
  • the env coding domain comprises an amphotropic env domain.
  • the env domain comprises a sequence from about nucleotide number 6359 to about nucleotide 8323 or a sequence having at least 95%, 98%, 99% or 99.8% (roundest to the nearest 10 th ) identity thereto.
  • 3' to the env termination codon is a therapeutic cassette comprising at least one core-promoter cassette and/or a mini-promoter cassette and may further include a polIII promoter cassette and/or an IRES cassette, each operably linked to heterologous domain (e.g., a sequence encoding a therapeutic molecule such as a polyeptpdie having cytosine deaminase or thymidine kinase activity).
  • the heterologous domain can comprise a cytosine deaminase or thymidine kinase of the disclosure.
  • the CD polynucleotide comprises a human codon optimized sequence.
  • the CD polynucleotide encodes a mutant polypeptide having cytosine deaminase, wherein the mutations confer increased thermal stabilization that increase the melting temperature (Tm) by 10°C allowing sustained kinetic activity over a broader temperature range and increased accumulated levels of protein.
  • the heterologous domain is a human codon optimized sequence comprising SEQ ID NO:75 and encoding a polypeptide having thymidine kinase activity.
  • the disclosure also provides a recombinant retroviral vector comprising from 5' to 3' a CMV-R-U5, fusion of the immediate early promoter from human cytomegalovirus to the MLV R-U5 region; a PBS, primer binding site for reverse transcriptase; a 5' splice site; a ⁇ packaging signal; a gag, ORF for MLV group specific antigen; a pol, ORF for MLV polymerase polyprotein; a 3' splice site; a 4070A env, ORF for envelope protein of MLV strain 4070A; a therapeutic cassette comprising at least one mini-promoter operably lined to a heterologous polynucleotide encoding a therapeutic molecule (e.g., a modified cytosine deaminase (thermostabilized and codon optimized)); a PPT, polypurine tract; and a U3-R-U5, MLV long terminal repeat.
  • the therapeutic methods e.g., the gene therapy or gene delivery methods
  • the therapeutic methods can be performed in vivo or ex vivo. It may be preferable to remove the majority of a tumor prior to gene therapy, for example surgically or by radiation.
  • the retroviral therapy may be preceded or followed by surgery, chemotherapy or radiation therapy.
  • steroids are co-administered with the vector (before, during or immediately after).
  • Example 1 Vector stability of emd.GFP and tk genes
  • a human glioma cell line U87-MG was cultured in complete culture medium. Naive cells were seeded at 2e5 cell per well in 6-well plates the day prior to infection. Vector from different plasmids was prepared by transient transfection on 293T cells and the supernatant is collected. Titers are measured as described ( WO2010036986 , Perez et al., Mol. Ther., 2012 ) typically around 10 ⁇ 6 TU/ml.
  • pAZ based vectors are similar to pAC3 based vectors, but the starting plasmid has an LTR promoter driving the whole viral RNA transcript rather than the hybrid CMV-LTR promoter ( Figure 8 .
  • the viral particles from both types of plasmid have complete MLV LTRs at both the 5' and 3' ends of the genome.
  • the first cycle of infection is performed at MOI 0.1 according to calculated titers (TU/mL) in the presence of 4pg/mL polybrene.
  • TU/mL calculated titers
  • one tenth of the viral supernatant produced by infected cells is used for infecting naive cells.
  • infected cells are passaged at d4 post infection into 6-well plates.
  • Viral supernatant from infected cells at d7 post infection is collected for subsequent infection, and cells are harvested for genomic extraction for assessment of vector stability by IRES-PCR.
  • the primers used for PCR are: IRES-F: 5'-CTGATCTTACTCTTTGGACCTTG-3'(SEQ ID NO:54) and IRES-R: 5'-CCCCTTTTTCTGGAGACTAAATAA-3' (SEQ ID NO:54).
  • the A1 and S1 promoters in the vectors expressing emd (GFP), derived from pAZ.A1.emd and pAZ.S1.emd appear a little more stable than vector derived from pAZ.C1.emd, but experience has shown that vectors stable to passage 6 in this test are useful, appear stable and, when armed with the appropriate gene, are therapeutic in mouse tumor models ( CR.
  • Example 2 Construction and configuration of pAC3 based vectors containing C1 and S1 core promoter driving GFP expression
  • the retroviral replicating vectors pAC3-C1.GFP and pAC3-S1.GFP, were derived from the backbone of pAC3-yCD2.
  • the pAC3 backbone was isolated by endonuclease digestion of the pAC3-yCD2 plasmid DNA with Mlu I and Not I.
  • the DNA sequence of C1.GFP and S1.GFP was isolated by endonuclease digestion of the pAZ-C1.GFP and pAZ.S1.GFP plasmid DNA, respectively, with Mlu I and Not I followed by insertion of the isolated DNA fragment to the corresponding restriction enzyme sites in the pAC3 backbone.
  • Example 3 Construction and configuration of pAC3 based vectors containing C1, S1 and S2 core promoter driving CD expression
  • the retroviral replicating vectors were derived from the backbone of pAC3-yCD2.
  • the pAC3 backbone was isolated by endonuclease digestion of the pAC3-yCD2 plasmid DNA with Mlu I and Not I.
  • the DNA sequence of C1.yCD2, S1.yCD2 and S2.yCD2 was synthesized with Mlu I and Not I restriction enzyme sites present at each end of the DNA fragment for subsequent cloning to the corresponding sites in the pAC3 backbone.
  • Example 4 Construction and configuration of pAC3 based vectors containing EMCV IRES and C1 or S1 core promoter driving hGMCSF and mGMCSF expression
  • the retroviral replicating vectors pAC3-hGMCSF and pAC3.S1-hGMCSF, pAC3-mGMCSF and pAC3.S1-mGMCSF (see, e.g., Figure 8 ), were derived from the backbone of pAC3-yCD2 vector (see, e.g., U.S. Pat. Publ. No. 20110217267A1 , incorporated herein by reference).
  • the pAC3 backbone in the vector was isolated by endonuclease digestion of the pAC3-yCD2 plasmid DNA with Psi I and Not I.
  • the cDNA sequence of human and mouse GMCSF gene, respectively, were synthesized with the Psi I and Not I restriction enzyme sites at each end of the DNA fragment and subsequently cloned into the corresponding site in the pAC3 backbone.
  • the pAC3 backbone in the vector was isolated by endonuclease digestion of the pAC3-yCD2 plasmid DNA with Mlu I and Not I.
  • S1-hGMCSF and S1-mGMCSF were synthesized with the Mlu I and Not I restriction enzyme sites at each end of the DNA fragment and subsequently cloned into the corresponding site in the pAC3 backbone.
  • Example 5 Vector stability and transgene expression of pAC3 based vectors containing C1 and S1 core promoter driving GFP expression
  • pAC3 based vectors with core promoters driving the expression of emerald GFP (pAC3-C1.emd and pAC3-S1.emd (emd a.k.a. GFP) were constructed as described and compared to pAC3.emd (aka pAC3-GFP, Perez et al., Mol. Ther. 2012 ), which is the equivalent vector using an internal IRES to drive expression of the emd.GFP gene.
  • Infectious vector was prepared by transient transfection as before. Early passage of a human glioma cell line U87-MG was cultured in complete culture medium. Naive cells were seeded at 2e5 cell per well in 6-well plates the day prior infection.
  • the first cycle of infection was performed at MOI 0.1 according to calculated titers (TU/mL) in the presence of 4pg/mL polybrene.
  • TU/mL calculated titers
  • one tenth of the viral supernatant produced by infected cells was used for infecting naive cells.
  • infected cells were passaged at d4 post infection into 6-well plates.
  • Viral supernatants from infected cells at d7 post infection were collected for subsequent infection, and cells were harvested for genomic extraction for assessment of vector stability by IRES-PCR.
  • the primers used for PCR were: IRES-F: 5'-CTGATCTTACTCTTTGGACCTTG-3' (SEQ ID NO:54) and IRES-R: 5'-CCCCTTTTTCTGGAGACTAAATAA-3' (SEQ ID NO:55).
  • the IRES dependent expression system showed about 5 fold higher levels of GFP expression in infected cells than the S1 promoter construct for all 3 different glioblastoma cell lines examined here, although absolute levels of expression also varied by a factor of about 5 over the three cell lines.
  • Example 6 Vector stability of pAC3-based vectors containing C1 and S1 core promoter driving CD expression and comparison to pACE-yCD2
  • pAC3 based vectors with core promoters driving the expression of CD were constructed as described and corresponding infectious vector preparations were compared to vector from pAC3.yCD2 ( O.D. Perez et al., Mol. Ther., 2012 ).
  • pAC3-C1.CD and pAC3-S1.CD were constructed as described and corresponding infectious vector preparations were compared to vector from pAC3.yCD2 ( O.D. Perez et al., Mol. Ther., 2012 ).
  • pAC3.yCD2 O.D. Perez et al., Mol. Ther., 2012 .
  • Early passage of a human glioma cell line U87-MG was cultured in complete culture medium. Naive cells were seeded at 2E5 cell per well in 6-well plates the day prior infection. The first cycle of infection was performed at MOI 0.1 according to calculated titers (TU/mL) in the presence of 4pg/mL polybrene.
  • infected cells were passaged at d4 post infection into 6-well plates.
  • Viral supernatant from infected cells at d7 post infection was collected for subsequent infection, and cells were harvested for genomic extraction for assessment of vector stability by IRES-PCR.
  • the primers used for PCR were: IRES-F: 5'-CTGATCTTACTCTTTGGACCTTG-3' (SEQ ID NO:54) and IRES-R: 5'-CCCCTTTTTCTGGAGACTAAATAA-3' (SEQ ID NO:55).
  • the relative stabilities are shown in Figure 2B and show that the C1.yCD2 vector is less stable than the other two vectors which are roughly equivalent in stability, with the S1.yCD2 vector apparently slightly more stable than the IRES vector (pAC3-yCD2).
  • Example 7 Transgene expression of pAC3-based vectors containing C1 and S1 core promoter driving CD expression and comparison to pAC3-yCD2, after transfection into 293T cells
  • the level of CD expression from the vectors after transfection in 293T cells was detected by immunoblotting using an antibody against CD ( Figure 4B ).
  • Naive cells were seeded at 2E6 cell per 10-cm plates the day prior transfection.
  • Transient transfection by calcium phosphate method was performed using plasmid DNA encoding the viral genome of each vector.
  • cells were harvested and lysed to obtain cell lysates. Protein concentration of cell lysates was determined to allow equal protein loading as indicated by GAPDH.
  • Figure 4B shows the results demonstrating expression from all these vectors with the IRES system yielding about 15 fold higher levels of expression than the S1 promoter construct.
  • Figure 4C shows a Western blot of cell extracts from U87 cells fully transduced with vector derived from pAC3-yCD2 in both pAC3-C1.yCD2 and pAC3-S1.yCD2. While the CD protein band is easily detectable for pAC3-yCD2, there was insufficient CD protein from cells infected with pAC3-C1.yCD2 and pAC3-S1.yCD2 to be detected in this assay.
  • Example 8 Replication kinetics, vector stability and transgene expression of pAC3 based vectors containing the IRES or S1 core promoter driving human and mouse GM-CSF expression
  • the replication kinetics of pAC3-IRES.hGMCSF, pAC3-S1.hGMCSF and pAC3-emd were assessed in U87-MG by qRT-PCR.
  • the replication kinetics of pAC3-IRES.mGMCSF, pAC3-S1.mGMCSF and pAC3-emd were assessed in EMT6 (a mouse breast cancer cell line). Naive cells were seeded at 1E5 cells (U87-MG) or 5E4 cells (EMT6) in 6-well plate the day prior infection.
  • Viral infection was performed at MOI 0.1 (U87-MG) or MOI 1 (EMT6) according to calculated titers (TU/mL) in the presence of 4pg/mL polybrene. Equal number of infected cells were seeded at each passage (every 2 days for U87-MG and 3-4 days for EMT6 cells) during the entire course of infection, and viral supernatant produced from infected cells at various time points is collected and stored in -80°C freezer. Samples of viral supernatant collected were processed to obtain viral RNA (Maxwell 16 LEV simplyRNA Cells Kit, Promega) followed by qRT-PCR. The number of viral RNA copies/ml at each time point is determined from a standard curve included in the qRT-PCR.
  • Viral supernatant from infected cells at d7 post infection was collected for subsequent infection, and cells were harvested for genomic extraction for assessment of vector stability by IRES-PCR.
  • the primers used for PCR are: IRES-F: 5'-CTGATCTTACTCTTTGGACCTTG-3' (SEQ ID NO:54) and IRES-R: 5'-CCCCTTTTTCTGGAGACTAAATAA-3' (SEQ ID NO:55).
  • the stability profiles on serial passage are shown in Figure 3 and demonstrate that the vector with the S1 promoter is at least as stable as the IRES-hGMCSF vector, while for the mouse GMCSF the S1 vector is more stable than the IRES version.
  • pAC3 based vectors with a core promoter driving the expression of human and mouse GM-CSF (pAC3-S1.hGMCSF and pAC3-S1.mGMCSF) were constructed and compared to pAC3-IRES.hGMCSF and pAC3-IRES.mGMCSF, respectively.
  • Vector preparations were made from the constructs by transient transfection as described.
  • the vector transfected 293T cells were assayed for production of hGMCSF and mGMCSF and Figure 4D and G show that expression of these proteins is observed in transfected cells, and that the transfected cells make about the same levels of human or mouse GMCSF from both the vector using the IRES expression system and the vectors using the S1 core promoter system, respectively.
  • Figure 4E and F show that hGMCSF expression driven by the S1 promoter is 3 fold less than the IRES configuration, in fully infected U87 and PC3 cells, respectively.
  • Figure 4H shows that in mouse EMT6 cells the S1 promoter is less efficient that the IRES vector in expressing mGMCSF after infection.
  • Example 9 Poor transgene expression of pAC3 based vectors containing C1 and S1 core promoters driving yCD2 relative to pAC3-yCD2
  • the levels of CD expression were detected in 293T cells by immunoblotting using an antibody against CD ( Figure 4B ).
  • Naive cells are seeded at 2E6 cell per 10-cm plates the day prior transfection.
  • Transient transfection by calcium phosphate method was performed using plasmid DNA encoding the viral genome of each vector.
  • cells are harvested and lysed to obtain cell lysates. Protein concentration of cell lysates is determined to allow equal protein loading as indicated by GAPDH.
  • Figure 4B shows the results demonstrating expression from all these vectors, with the IRES system yielding about 15 fold higher levels of expression than the S1 promoter construct.
  • Figure 4C shows expression of CD protein in an immunoblot in fully infected U87-MG cells from cells infected with vector from pAC3-yCD2 (IRES vector) but undetectable expression of yCD2 in both C1. yCD2 and S1.yCD2 vectors.
  • Example 10 In vitro positive selection using pAC3-S1.yCD2 vector in human cells to increase yCD2 expression
  • Positive selection of fully infected pAC3.S1.yCD2 vector is performed by concurrently giving N-(phosphonacetyl)-L-aspartate (PALA), an inhibitor of pyrimidine de novo synthesis, which leads to pyrimidine depletion-mediated cell death of non-infected cells or cells expression low level of yCD2.
  • PHA N-(phosphonacetyl)-L-aspartate
  • cytosine With addition of cytosine in culture, it rescues cells expression high level of yCD2 gene via the pyrimidine salvage pathway.
  • the method described below applies to a U87 glioblastoma derived cell line used in the laboratory, but the same procedures can be used with multiple different cell lines derived from different tumor types.
  • the actual concentrations of reagents and timing of the steps will be determined by the rate of growth of the cells and the initial infection rates of the cell line. Such adjustments can be made as needed by one skilled in the art and will be determined in the course of performing the method. In addition this optimization procedure can be used with any promoter driving a selectable gene in a replicating vector. Also other variations in actual reagent concentrations and timing of selection may be possible.
  • the concentration PALA required to kill naive U87 cells was first determined, U87 cells infected with pAC3-yCD2 vector and for U87 cells with pAC3.S1-yCD2 vector. Cell were seeded at 3E3 cells in 96-well plates the day before. At 24 hour post cell seeding, PALA at 0.00975, 0.039, 0.156, 0.625, 2.5, 10, 40 and 160 uM were added to the culture for 5 consecutive days followed by an MTS assay to determine the cell viability.
  • Figure 6 shows that the IC 50 of PALA ranges between 8-30 uM.
  • a range of cytosine concentrations (0.2, 1, 5 10 mM) in culture was also determined by performing the same experiment described above. This shows that the cells can tolerate cytosine in all concentrations tested.
  • naive U87 cells are seeded at 1e5 cells in 6-well plates the day before. The next day, the cells are infected with pAC3-yCD2 vector (positive control) and separately with pAC3.S1-yCD2 vector, respectively, at MOI of 0.1.
  • PALA at 1 uM and cytosine at 10 mM are added to the culture containing naive U87 cells (negative control), U87 cells infected with pAC3-yCD2 vector (positive control) and U87 cells with pAC3.S1-yCD2 for 5 consecutive days at which time point, the culture supernatant is collected for a new round of infection with naive U87 cells.
  • the infection cycle in the presence of PALA and cytosine is repeated for 12 rounds with increasing concentration of PALA cycle 1-2: 1 uM; cycle 3-4: 3.3 uM; cycle 5-6: 10 uM, cycle 7-8: 20 uM and cycle 9-12: 30 uM).
  • cells are isolated and expanded in the presence of 30 uM PALA and 10 mM cytosine.
  • MTS assay is performed to demonstrate the increase of cell viability as a result of the positive selection.
  • Cells infected with pAC3.S1.yCD2 vector prior to selection are not able to efficiently utilize the salvage pathway due to low CD expression.
  • cells infected with pAC3.S1-yCD2 vector post selection show high cell viability that is comparable to cells infected with pAC3-yCD2 vector.
  • IRES-F 5'-CTGATCTTACTCTTTGGACCTTG-3' (SEQ ID NO:54) and IRES-R: 5'-CCCCTTTTTCTGGAGACTAAATAA-3'(SEQ ID NO:55).
  • the resulting PCR products are isolated for PCR cloning for sequencing analysis. The sequencing result show that multiple mutations occur in the S1 core promoter. Subsequently, the S1 promoter with identified mutations is synthesized with Mlu I and Not I site at each end of the DNA fragment for subcloning into pAC3 backbone as described above. The resulting vector with optimized S1 promoter is designated pAC3.mtS1-yCD2.
  • Infectious pAC3.mtS1-yCD2 vector is prepared by transient transfection in 293T cells as before. Naive U87 cells are infected with pAC3.mtS1-yCD2 vector at MOI of 0.1. At day 7 post infection, cells are harvested and lysed to obtain cell lysates. Protein concentration of cell lysates is determined to allow equal protein loading as indicated by GAPDH in the immunoblot. The data show that the CD expression of cell extracts from U87 cells infected with pAC3.mtS1-yCD2 vector is comparable to that of pAC3-yCD2 vector driven by the IRES.
  • U87 cells with no vector, with pAC3-yCD2 vector, and pAC3.mtS1-yCD2 vector, respectively, are seeded at 1e3 cells per well in 96-well plates. They are monitored over an eight day period following treatment with various concentrations of 5-FC, which is first added one day after plating and then replenished with whole medium plus 5-FC every two days. Cell viability is assessed every two days by MTS assay.
  • IC50 value for U87 cells infected with pAC3.mtS1-yCD2 vector is comparable to those infected with pAC3-yCD2 vector (0.5 ug/mL; Perez et al., 2012).
  • Other promoter configurations can be optimized for gene expression using these techniques.
  • Example 11 Incorporation of Kozak sequence downstream of the core promoter increases yCD2 gene expression without altering vector stability
  • eukaryotic mRNAs contain Kozak sequence which facilitates initiation of protein translation. Incorporation of Kozak sequence downstream of the core promoter increases yCD2 expression in both transiently transfected and fully infected cells.
  • the optimized yeast CD gene, yCD2 has 3 in-frame ATG within the first 15 amino acids in the coding region. The spacing in the 5'UTR and the lack of Kozak sequence flanking the initiation codon in yCD2 mRNA was considered suboptimal for efficient protein translation initiation. Incorporation of Kozak sequence and/or other translational enhancer element may greatly improve the translation initiation and thus protein production of transgenes.
  • the pAC3.S1-yCD2 vector contains a core promoter without Kozak sequence. Although the core promoter has demonstrated useful transcription, efficient protein translation is equally important to confer gene expression. This improvement can be combined with others in this specification for improved core promoters or other improved minipromoters.
  • the pAC3-kozakS1.yCD2, (AKA pAC3.S1K-yCD2) and pAC3.kozakS2-yCD2 (AKA pAC3.S2K-yCD2) are derived from the backbone of pAC3-yCD2.
  • the pAC3 backbone is isolated by endonuclease digestion of the pAC3-yCD2 plasmid DNA with Mlu I and Not I.
  • the DNA sequence of kozakS1yCD2 and kozakS2yCd2 are synthesized with Mlu I and Not I restriction enzyme site present at each end of the DNA fragment for subsequent cloning to the corresponding sites in the pAC3 backbone.
  • Infectious vectors are prepared by transient transfection in 293T cells as before.
  • Naive U87 cells are infected with vectors at MOI of 0.1.
  • cells are harvested and lysed to obtain cell lysates. Protein concentration of cell lysates is determined to allow equal protein loading as indicated by GAPDH in the immunoblot.
  • Figure 4B shows that the CD expression of cell extracts from 293T transiently transfected with pAC3.S1K-yCD2 vector is approximately 2-5 higher than pAC3.S1-yCD2 vector.
  • CD expression of pAC3.S2K-yCD2 is approximately 2-5 higher than pAC3-S2-yCD2 vector in transiently transfected 293T cells.
  • CD expression is comparable between pAC3-S1K-yCD2 and pAC3-S2K-yCD2 in transiently transfected 293T cells.
  • Figure 4C shows CD expression is undetectable in maximally infected U87 cells with any one of the four vectors.
  • U87 cells with no vector, with pAC3-yCD2 vector, and pAC3-kozakS1.yCD2 vector, respectively, are seeded at 1E3 cells per well in 96-well plates. They are monitored over an eight day period following treatment with various concentrations of 5-FC, which is first added one day after plating and then replenished with whole medium plus 5-FC every two days. Cell viability is assessed every two days by MTS assay.
  • IC 50 value for U87 cells infected with pAC3-kozakS1.yCD2 vector is approximately 5 fold higher than those infected with pAC3-S1.yCD2 vector, and within 10 fold of the pAC3-yCD2 vector (0.5 ug/mL; Perez et al., 2012).
  • naive U87 cells are seeded at 2E5 cell per well in 6-well plates the day prior infection.
  • the first cycle of infection is performed at MOI 0.1 according to calculated titers (TU/mL) in the presence of 4pg/mL polybrene.
  • TU/mL calculated titers
  • one tenth of the viral supernatant produced by infected cells is used for infecting naive cells.
  • infected cells were passaged at d4 post infection into 6-well plates.
  • Viral supernatants from infected cells at d7 post infection were collected for subsequent infection, and cells were harvested for genomic extraction for assessment of vector stability by IRES-PCR.
  • the primers used for PCR were: IRES-F: 5'-CTGATCTTACTCTTTGGACCTTG-3' (SEQ ID NO:54) and IRES-R: 5'-CCCCTTTTTCTGGAGACTAAATAA-3' (SEQ ID NO:55).
  • the data show that the stability of pAC3.kozakS1-yCD2 vector is comparable to that of pAC3-yCD2 and pAC3.S1-yCD2 vector.
  • Example 12 Construction and configuration of pAC3 based vectors containing optimized S1 core promoter driving yCD2-UPRT
  • the yCD2-UPRT is ⁇ 1.2 kb.
  • the mtS1 promoter optimized S1 promoter (see Example 11).
  • the pAC3-mtS1.yCD2-UPRT vector is derived from the backbone of pAC3-yCD2.
  • the pAC3 backbone is isolated by endonuclease digestion of the pAC3-yCD2 plasmid DNA with Mlu I and Not I.
  • the DNA sequence of mtS1.yCD2-UPRT is synthesized with Mlu I and Not I restriction enzyme site present at each end of the DNA fragment for subsequent cloning to the corresponding sites in the pAC3 backbone.
  • Example 13 Vector stability and transgene expression of pAC3 based vectors containing optimized S1 core promoter driving yCD2-UPRT expression
  • pAC3 based vectors with optimized core promoters driving the expression of yCD2-UPRT are constructed using similar techniques as above and compared to pAC3-yCD2-U (aka T50003, Perez et al., Mol.Ther., 2012 , WO2010045002 ), which is the equivalent vector using an internal IRES to drive expression of the yCD2-UPRT fusion gene.
  • Infectious pAC3-mtS1.yCD2-UPRT vector is prepared by transient transfection in 293T cells. Naive U87 cells infected with pAC3kozakS1.yCD2 vector at MOI of 0.1. At day 7 post infection, cells are harvested and lysed to obtain cell lysates. Protein concentration of cell lysates is determined to allow equal protein loading as indicated by GAPDH in the immunoblot. The data show that the CD-UPRT expression ( ⁇ 44KDa) from cell extracts of U87 cells infected with pAC3-mtS1.yCD2-UPRT vector is comparable to pAC3-yCD2-U and pAC3-yCD2 vectors.
  • U87 cells with no vector, with pAC3-yCD2, pAC3-yCD2-U, and pAC3-mtS1.yCD2-UPRT vector, respectively, are seeded at 1E3 cells per well in 96-well plates. They are monitored over an eight day period following treatment with various concentrations of 5-FC, which is first added one day after plating and then replenished with whole medium plus 5-FC every two days. Cell viability is assessed every two days by MTS assay. The data show that IC 50 value for U87 cells infected with pAC3-mtS1.yCD2-UPRT vector is at least equivalent to those infected with pAC3-yCD2 and pAC3-yCD2-U vectors.
  • naive U87 cells are seeded at 2E5 cell per well in 6-well plates the day prior infection.
  • the first cycle of infection is performed at MOI 0.1 according to calculated titers (TU/mL) in the presence of 4pg/mL polybrene.
  • TU/mL calculated titers
  • one tenth of the viral supernatant produced by infected cells is used for infecting naive cells.
  • infected cells were passaged at d4 post infection into 6-well plates.
  • Viral supernatants from infected cells at d7 post infection were collected for subsequent infection, and cells were harvested for genomic extraction for assessment of vector stability by IRES-PCR.
  • the primers used for PCR were: IRES-F: 5'-CTGATCTTACTCTTTGGACCTTG-3' (SEQ ID NO:56) and IRES-R: 5'-CCCCTTTTTCTGGAGACTAAATAA-3' (SEQ ID NO:57).
  • IRES-F 5'-CTGATCTTACTCTTTGGACCTTG-3'
  • IRES-R 5'-CCCCTTTTTCTGGAGACTAAATAA-3'
  • Example 14 Construction and configuration of pAC3-based vectors containing optimized S1 core promoter driving yCD2 expression and human U6 (Pol III) promoter driving shRNA against TGFb2
  • the pAC3-S1.yCD2-polIII promoter-shRNATGFb2 vector is derived from the backbone of pAC3-yCD2.
  • the pAC3 backbone is isolated by endonuclease digestion of the pAC3-yCD2 plasmid DNA with Mlu I and Not I.
  • the DNA sequence of mtS1.yCD2 and polIII promoter-shRNATGFb2 is synthesized with Mlu I and Not I restriction enzyme site present at each end of the DNA fragment for subsequent cloning to the corresponding sites in the pAC3 backbone.
  • Example 15 Vector stability and transgene expression of pAC3 based vectors containing optimized S1 core promoter driving yCD2 expression and human pol III promoter promoter driving shRNA against TGFb2
  • Infectious pAC3-mtS1.yCD2-polIII promoter-shRNATGFb2 vector is prepared by transient transfection in 293T cells as before. Naive U87 cells infected with pAC3-kozakS1.yCD2 vector at MOI of 0.1. At day 7 post infection, one portion of cells are harvested and lysed to obtain cell lysates, and another portion of cells are harvested for total RNA extraction. Protein concentration of cell lysates is determined to allow equal protein loading as indicated by GAPDH in the immunoblot.
  • U87 cells with no vector, with pAC3-yCD2, and pAC3-mtS1.yCD2-polIII promoter-shRNATGFb2 vector, respectively, are seeded at 1E3 cells per well in 96-well plates. They are monitored over an eight day period following treatment with various concentrations of 5-FC, which is first added one day after plating and then replenished with whole medium plus 5-FC every two days. Cell viability is assessed every two days by MTS assay.
  • RNA is extracted from cells harvested at d7 post infection as described above.
  • Gene expression of TGFb2 is measured by qRT-PCR using RNA polIII promoter as an internal control for normalization.
  • the relative expression level of TGFb2 to naive U87 cells is calculated using ⁇ C(t) method. The data show that at d7 post infection, more than 70% of TGFb2 is downregulated. The infected cells were cultured up to 30 days and observe sustained knockdown of TFGb2.
  • naive U87 cells were seeded at 2E5 cell per well in 6-well plates the day prior infection.
  • the first cycle of infection was performed at MOI 0.1 according to calculated titers (TU/mL) in the presence of 4pg/mL polybrene.
  • TU/mL calculated titers
  • one tenth of the viral supernatant produced by infected cells was used for infecting naive cells.
  • infected cells were passaged at d4 post infection into 6-well plates.
  • Viral supernatants from infected cells at d7 post infection were collected for subsequent infection, and cells were harvested for genomic extraction for assessment of vector stability by IRES-PCR.
  • the primers used for PCR were: IRES-F: 5'-CTGATCTTACTCTTTGGACCTTG-3'(SEQ ID NO:54) and IRES-R: 5'-CCCCTTTTTCTGGAGACTAAATAA-3' (SEQ ID NO:55).
  • the data show that stability of pAC3-mtS1.yCD2-polIII promoter-shRNATGFb2 vector is comparable to pAC3-yCD2 and pAC3-mtS1.yCD2 vectors.
  • Example 16 Construction and configuration of pAC3-based vectors containing optimized S1 core promoter driving yCD2 expression and optimized S1 core promoter driving tko.
  • the pAC3-mtS1.yCD2-mtS1.tko vector is derived from the backbone of pAC3-yCD2.
  • the pAC3 backbone is isolated by endonuclease digestion of the pAC3-yCD2 plasmid DNA with Mlu I and Not I.
  • the DNA sequence of mtS1.yCD2-mtS1.tko is synthesized with Mlu I and Not I restriction enzyme site present at each end of the DNA fragment for subsequent cloning to the corresponding sites in the pAC3 backbone.
  • Example 17 Vector stability and transgene expression of pAC3 based vectors containing an optimized S1 core promoter driving yCD2 expression and an optimized S1 core promoter driving tko.
  • Infectious pAC3-mtS1.yCD2-mtS1.tko vector is prepared by transient transfection in 293T cells as before. Naive U87 cells infected with pAC3-kozakS1.yCD2 vector at MOI of 0.1. At day 7 post infection, cells are harvested and lysed to obtain cell lysates, Protein concentration of cell lysates is determined to allow equal protein loading as indicated by GAPDH in the immunoblot. The data show that the yCD2 and TK expression from cell extracts of U87 cells infected with pAC3-mtS1.yCD2-mtS1.tko vector is comparable to those from pAC3-yCD2 and pAC3-tko vectors mediated by IRES.
  • U87 cells with no vector, with pAC3-yCD2, and pAC3-mtS1.yCD2-mtS1.tko vector, respectively, are seeded at 1E3 cells per well in 96-well plates. They are monitored over an eight day period following treatment with various concentrations of 5-FC, which is first added one day after plating and then replenished with whole medium plus 5-FC every two days. Cell viability is assessed every two days by MTS assay. The data show that IC 50 value for U87 cells infected with pAC3-mtS1.yCD2-mtS1.tko vector is comparable to those infected with pAC3-yCD2 vector.
  • U87 cells with no vector, with pAC3-tko, and pAC3-mtS1.yCD2-mtS1.tko vector, respectively, are seeded at 1e3 cells per well in 96-well plates. They are monitored over an eight day period following treatment with various concentrations of ganciclovir, which is first added one day after plating and then replenished with whole medium plus ganciclovir every two days. Cell viability is assessed every two days by MTS assay. The data show that IC50 value for U87 cells infected with pAC3-mtS1.yCD2-mtS1.tko vector is comparable to those infected with pAC3-tko vector.
  • naive U87 cells are seeded at 2E5 cell per well in 6-well plates the day prior infection.
  • the first cycle of infection is performed at MOI 0.1 according to calculated titers (TU/mL) in the presence of 4pg/mL polybrene.
  • TU/mL calculated titers
  • one tenth of the viral supernatant produced by infected cells is used for infecting naive cells.
  • infected cells are passaged at d4 post infection into 6-well plates.
  • Viral supernatants from infected cells at d7 post infection are collected for subsequent infection, and cells are harvested for genomic extraction for assessment of vector stability by IRES-PCR.
  • the primers used for PCR were: IRES-F: 5'-CTGATCTTACTCTTTGGACCTTG-3' (SEQ ID NO:54) and IRES-R: 5'-CCCCTTTTTCTGGAGACTAAATAA-3' (SEQ ID NO:55).
  • IRES-F 5'-CTGATCTTACTCTTTGGACCTTG-3'
  • IRES-R 5'-CCCCTTTTTCTGGAGACTAAATAA-3'
  • Example 18 Construction, configuration and testing of pAC3 based vectors, pAC3-HOE1.yCD2, pAC3-HOE2.yCD etc. containing a hybrid promoter with the human hemoxygenase gene core promoter, selected enhancer segments and a Kozak sequence, driving expression of the yCD2 gene.
  • the pAC3 backbone in the vector was isolated by endonuclease digestion of the pAC3-yCD2 plasmid DNA with Mlu I and Not I.
  • a sequence corresponding to the human heme oxygenase 1 gene core promoter fused with a Kozak start site and the yCD2 gene is synthesized with a Not1 site on the 3' end and a Mlu1 site on the 5' end and digested with both enzymes.
  • the synthesized fragment is : where the large C is the transcription start site, the first underlined sequence is the Kozak sequence including the ATG start codon (italics) of the yCD2 gene, and the second underlined sequence is the stop codon for yCD2.
  • This fragment is 625 nucleotides, with a 126bp fragment upstream of the transcription start site which is the heme oxygenase promoter.
  • This fragment is ligated to the pAC3Mlu1-Not backbone fragment isolated above, in the presence of excess of the Mlu1 fragments carrying the transcription factor binding site mixtures, and individual clones isolated by bacterial transfections followed by analyses of restriction digest of DNA mini-preps to identify plasmids with the pAC3 backbone the heme oxygenase promoter and CD, and a single copy of the binding site mix, below about 200bp.
  • the plasmids that carry the desired sequences are then used to make infectious vector by transient transfection and U87 cells infected and assayed by Western blot for CD protein.
  • Vectors expressing equivalent CD protein to pAC3-yCD2 or above are identified and sequenced to characterize the transcription factor binding site mix. Suitable identified binding site mixes as small as 40 bp are used to make vectors with other genes. Stability of the vectors are tested by serial passage as before.
  • the ligation mix of transcription factor binding sites, core promoter-CD and pAC3 back bone is used with the PALA selection method in target cells such as U87, to select vectors that express high levels of CD protein.
  • Example 19 Construction, configuration and testing of pAC3 based vectors, pAC3-cTK.yCD2,. containing a hybrid promoter with the Herpes Virus 1thymidine kinase gene promoter, selected enhancer segments and a Kozak sequence, driving expression of the yCD2 gene.
  • the Herpes Thymidine Kinase gene sequence is known to have a cryptic core promoter between the first and third ATG of the normal mRNA coding sequence ( Al-shawi et al. Mol. Cell. Biol. 11: 4207 1991 , Salamon et al Mol. Cell. Biol. 15:5322 1995 ).
  • This 180bp sequence is co-synthesized with both enhancers such as those mixtures isolated in example 18 or in this case with the 72 bp enhancer repeats from SV40 ( Gruss et al PNAS 78: 943-9471981 , NCBI Reference Sequence: NC_001669.1) a single copy of which is:
  • the total synthesized sequence has MLu1 and Not1 sites on the 5' and 3' ends respectively and is inserted into the pAC3 MLu1-Not 1 backbone fragment isolated as in example 18.
  • the ligation mix is used to transfect bacteria and desired molecular clones isolated and tested for stability and CD expression by Western blot as described in example X. Levels of CD expression are as least as good as for pAC3-yCD2.
  • Example 20 Construction, configuration and testing of transgene expression of pAC3 based vectors containing SV40 promoter, RSV promoter, a synthetic promoter with selected enhancer segments.
  • the pAC3 backbone in the vector was isolated by endonuclease digestion of the pAC3-yCD2 plasmid DNA with Mlu I and Not I sites as described above or by endonuclease digestion of the pAC3-Gluc plasmid DNA with Mlu I and Psi I sites.
  • the retroviral replicating vectors pAC3-SV40-GFP-R, pAC3-SV40-Gluc, pAC3-RSV-Gluc, and pAC3.ES1-Gluc were derived from the backbone of pAC3-yCD2.
  • the pAC3 backbone was isolated by endonuclease digestion of the pAC3-yCD2 plasmid DNA with Mlu I and Not I.
  • the DNA sequence of SV40-GFP-R was synthesized or amplified by polymerase chain reaction (PCR) with Mlu I and Psi I at each end of DNA fragment for subcloning into the pAC3-Gluc backbone to replace the IRES sequence at the corresponding restriction sites.
  • the SV40-GFP cassette was placed in a reversed orientation in the 3'UTR to minimize promoter interference in proviral DNA configuration.
  • pAC3-SV40-GFP-R viruses are prepared by transient transfection in 293T cells as before. Naive U87 cells are infected with these vectors at MOI of 0.01. At day 13 post infection, cells are harvested and analyzed by flow cytometry by gating GFP-positive cells and measuring the mean fluorescent intensity of the GFP-positive population.
  • Figure 7 shows that the GFP expression level of pAC3-SV40-GFP-R is higher than pAC3-S1-GFP, but still significantly less than that of pAC3-GFP mediated by IRES.
  • pAC3-Gluc, pAC3-SV40-Gluc, pAC3-RSV-Gluc, and pAC3.ES1-Gluc viruses are prepared by transient transfection in 293T cells as before. Naive U87 cells are infected with these vectors at MOI of 0.01. Supernatant from each cell passage (day 3, day 6 and day 9 post infection) is collected. At each cell passage, same number of cells are seeded and cultured in equal volume of culture medium. A 1:5 serial dilutions of the supernatant of each sample from each time point are made to measure the intensity of luminescence in the presence of the substrate, colenterazine, at a final concentration of 15 uM. The data show that Gluc expression levels mediated by SV40, RSV, and ES1 promoters are 2-3 times less than that mediated by IRES.
  • Example 21 Construction, configuration and testing of transgene expression of pAC3 based vectors containing RSV promoter, SV40 promoter, S1 core promoter, EC1 synthetic promoter and ES1 synthetic promoter.
  • the pAC3 backbone in the vector was isolated by endonuclease digestion of the pAC3-yCD2 plasmid DNA with Mlu I and Not I sites as described above or by endonuclease digestion of the pAC3-Gluc plasmid DNA with Mlu I and Psi I sites.
  • the retroviral replicating vectors, pAC3-SV40-Gluc, pAC3-RSV-Gluc, and pAC3.ES1-Gluc were derived from the backbone of pAC3-yCD2.
  • the pAC3 backbone was isolated by endonuclease digestion of the pAC3-yCD2 plasmid DNA with Mlu I and Not I.
  • the DNA sequence of SV40-GFP-R, SV40-Gluc, RSV-Gluc, and ES1-Gluc, respectively, were synthesized or amplified by polymerase chain reaction (PCR) with Mlu I and Psi I at each end of DNA fragment for subcloning into the pAC3-Gluc backbone to replace the IRES sequence at the corresponding restriction sites.
  • PCR polymerase chain reaction
  • the SV40-GFP cassette was placed in a reversed orientation in the 3'UTR to minimize promoter interference in proviral DNA configuration.
  • RVS promoter is 271 nts in length; SV40 promoter is 324 nts in length.
  • Synthetic S1 core promoter is 80 nts in length.
  • EC1 which is a hybrid promoter consists of tandem repeats of CRE ( Schlabach et al., 2010 PNAS ) and the C1 core promoter ( Juven-Gershon et al., 2006 Nature Methods )is 181 nts in length.
  • ES1 which is hybrid of tandem repeats of CRE and S1 core promoter ( Juven-Gershon et al., 2006 Nature Methods ) is 188 nts in length.
  • Gluc expression from pAC3-Gluc, pAC3-RSV-Gluc, pAC3-SV40-Gluc, pAC3-EC1-Gluc, pAC3-S1-Gluc and pAC3-ES1-Gluc were evaluated in transiently transfected 293T or Hela cells. At 48 hours post transfection, the supernatant was collected and Gluc expression level is determined by co-incubation of 1:3 or 1:4 serially diluted supernatant with colenterazine at a final concentration of 15 uM.
  • Gluc expression levels mediated by RSV is approximately 3 fold higher than Gluc expression mediated by IRES.
  • Gluc expression level mediated by SV40, EC1 and promoters are comparable to that of IRES.
  • Gluc expression mediated by S1 core promoter is 3-fold less than that of IRES.
  • the promoter activity is about 1/3 less than IRES and EC1, but 2-fold higher than S1 alone.
  • Gluc expression levels mediated by RSV, SV40, and ES1 is approximately 2.5 fold lower than Gluc expression mediated by IRES.
  • the disparity of the RSV results wth those seen in 293T cells (3 fold greater than IRES) is expected as, although the RSV LTR promoter is known to be ubiquitously expressed, unusually, in Hela cells it is specifically suppressd by a 21kD inhibitory protein, not present in most other cell types.
  • the Gluc expression level mediated by the S1 core promoter alone is approximately 10-fold less than that mediated by IRES.
  • inclusion of the synthetic enhancer (ES1) increases the promoter activity by 4-fold.
  • the Gluc expression level mediated by EC1 is slightly higher than that mediated by IRES ( Figure 9 ).
  • pAC3-Gluc, pAC3-CMV-Gluc, pAC3-RSV-Gluc, and pAC3-SV40-Gluc viruses are prepared by transient transfection in 293T cells as before. Naive U87 cells are infected with these vectors at MOI of 0.01. Supernatant from each cell passage (day 3, day 6 and day 9 post infection) is collected. At each cell passage, same number of cells are seeded and cultured in equal volume of culture medium. A 1:3 serial dilutions of the supernatant of each sample from each time point are made to measure the intensity of luminescence in the presence of the substrate, colenterazine, at a final concentration of 15 uM. The data show that Gluc expression levels mediated by RSV, SV40, EC1 and ES1 promoters are comparable to that mediated by IRES.

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